partis-bcr 1.0.11.post1.dev3__cp312-cp312-manylinux1_x86_64.whl → 1.0.11.post1.dev7__cp312-cp312-manylinux1_x86_64.whl

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
Files changed (57) hide show
  1. bin/partis-test.py +3 -3
  2. {partis_bcr-1.0.11.post1.dev3.data → partis_bcr-1.0.11.post1.dev7.data}/scripts/partis-test.py +3 -3
  3. {partis_bcr-1.0.11.post1.dev3.dist-info → partis_bcr-1.0.11.post1.dev7.dist-info}/METADATA +1 -1
  4. {partis_bcr-1.0.11.post1.dev3.dist-info → partis_bcr-1.0.11.post1.dev7.dist-info}/RECORD +57 -56
  5. test/new-results/partition-new-simu/fasttree/iclust-0/log +3 -3
  6. test/new-results/run-times.csv +4 -4
  7. test/new-results/test/simu.yaml +1 -1
  8. test/new-results/test.log +24 -24
  9. test/paired/new-results/partition-new-simu/fasttree/iclust-0/log +2 -2
  10. test/paired/new-results/partition-new-simu/fasttree/iclust-1/log +4 -4
  11. test/paired/new-results/partition-new-simu/fasttree/iclust-2/log +4 -4
  12. test/paired/new-results/partition-new-simu-annotation-performance/plots/flcount-matrix.svg +107 -107
  13. test/paired/new-results/partition-new-simu-annotation-performance/plots/func-non-func-per-drop-log.svg +83 -83
  14. test/paired/new-results/partition-new-simu-annotation-performance/plots/func-non-func-per-drop.svg +61 -61
  15. test/paired/new-results/partition-new-simu-annotation-performance/plots/paired-seqs-per-seq-after.svg +18 -18
  16. test/paired/new-results/partition-new-simu-annotation-performance/plots/paired-seqs-per-seq-before.svg +24 -24
  17. test/paired/new-results/partition-new-simu-annotation-performance/plots/pseq-matrix.svg +35 -35
  18. test/paired/new-results/partition-new-simu-annotation-performance/plots/seqs-per-droplet.svg +22 -22
  19. test/paired/new-results/partition-new-simu-annotation-performance/plots/true-pair-clean-performance-correct-family.svg +45 -45
  20. test/paired/new-results/partition-new-simu-annotation-performance/plots/true-pair-clean-performance-correct.svg +45 -45
  21. test/paired/new-results/partition-new-simu-annotation-performance/plots/true-pair-clean-performance-mispaired.svg +45 -45
  22. test/paired/new-results/partition-new-simu-annotation-performance/plots/true-pair-clean-performance-multiple.svg +15 -15
  23. test/paired/new-results/partition-new-simu-annotation-performance/plots/true-pair-clean-performance-near-family.svg +15 -15
  24. test/paired/new-results/partition-new-simu-annotation-performance/plots/true-pair-clean-performance-total.svg +47 -47
  25. test/paired/new-results/partition-new-simu-annotation-performance/plots/true-pair-clean-performance-unpaired.svg +48 -48
  26. test/paired/new-results/partition-new-simu-annotation-performance/plots/true-pair-clean-performance.svg +27 -27
  27. test/paired/new-results/run-times.csv +7 -7
  28. test/paired/new-results/subset-partition-new-simu/isub-0/partition.log +2 -2
  29. test/paired/new-results/subset-partition-new-simu/isub-1/partition.log +2 -2
  30. test/paired/new-results/subset-partition-new-simu/merged-partition.log +3 -3
  31. test/paired/new-results/subset-partition-new-simu/merged-subsets/parameters/igh/sw-cache.yaml +1 -1
  32. test/paired/new-results/subset-partition-new-simu/merged-subsets/parameters/igk/sw-cache.yaml +1 -1
  33. test/paired/new-results/subset-partition-new-simu/merged-subsets/parameters/igl/sw-cache.yaml +1 -1
  34. test/paired/new-results/test/simu/all-seqs.fa +168 -212
  35. test/paired/new-results/test/simu/igh+igk/igh.yaml +1 -1
  36. test/paired/new-results/test/simu/igh+igk/igk.yaml +1 -1
  37. test/paired/new-results/test/simu/igh+igl/igh.yaml +1 -1
  38. test/paired/new-results/test/simu/igh+igl/igl.yaml +1 -1
  39. test/paired/new-results/test/simu/igh.yaml +1 -1
  40. test/paired/new-results/test/simu/igk.yaml +1 -1
  41. test/paired/new-results/test/simu/igl.yaml +1 -1
  42. test/paired/new-results/test/simu/meta.yaml +1 -1
  43. test/paired/new-results/test.log +97 -109
  44. test/test.py +3 -3
  45. test/trees.nwk +100 -0
  46. {partis_bcr-1.0.11.post1.dev3.data → partis_bcr-1.0.11.post1.dev7.data}/scripts/cf-alleles.py +0 -0
  47. {partis_bcr-1.0.11.post1.dev3.data → partis_bcr-1.0.11.post1.dev7.data}/scripts/cf-germlines.py +0 -0
  48. {partis_bcr-1.0.11.post1.dev3.data → partis_bcr-1.0.11.post1.dev7.data}/scripts/compare-plotdirs.py +0 -0
  49. {partis_bcr-1.0.11.post1.dev3.data → partis_bcr-1.0.11.post1.dev7.data}/scripts/extract-pairing-info.py +0 -0
  50. {partis_bcr-1.0.11.post1.dev3.data → partis_bcr-1.0.11.post1.dev7.data}/scripts/gctree-run.py +0 -0
  51. {partis_bcr-1.0.11.post1.dev3.data → partis_bcr-1.0.11.post1.dev7.data}/scripts/get-naive-probabilities.py +0 -0
  52. {partis_bcr-1.0.11.post1.dev3.data → partis_bcr-1.0.11.post1.dev7.data}/scripts/parse-output.py +0 -0
  53. {partis_bcr-1.0.11.post1.dev3.data → partis_bcr-1.0.11.post1.dev7.data}/scripts/split-loci.py +0 -0
  54. {partis_bcr-1.0.11.post1.dev3.dist-info → partis_bcr-1.0.11.post1.dev7.dist-info}/WHEEL +0 -0
  55. {partis_bcr-1.0.11.post1.dev3.dist-info → partis_bcr-1.0.11.post1.dev7.dist-info}/entry_points.txt +0 -0
  56. {partis_bcr-1.0.11.post1.dev3.dist-info → partis_bcr-1.0.11.post1.dev7.dist-info}/licenses/COPYING +0 -0
  57. {partis_bcr-1.0.11.post1.dev3.dist-info → partis_bcr-1.0.11.post1.dev7.dist-info}/top_level.txt +0 -0
test/new-results/test/simu.yaml CHANGED
@@ -1 +1 @@
1
- {"version-info": {"partis-yaml": 0.1, "partis-git": ""}, "germline-info": {"locus": "igh", "functionalities": {}, "seqs": {"v": {"IGHV1-18*01": "CAGGTTCAGCTGGTGCAGTCTGGAGCTGAGGTGAAGAAGCCTGGGGCCTCAGTGAAGGTCTCCTGCAAGGCTTCTGGTTACACCTTTACCAGCTATGGTATCAGCTGGGTGCGACAGGCCCCTGGACAAGGGCTTGAGTGGATGGGATGGATCAGCGCTTACAATGGTAACACAAACTATGCACAGAAGCTCCAGGGCAGAGTCACCATGACCACAGACACATCCACGAGCACAGCCTACATGGAGCTGAGGAGCCTGAGATCTGACGACACGGCCGTGTATTACTGTGCGAGAGA", "IGHV1-2*02": "CAGGTGCAGCTGGTGCAGTCTGGGGCTGAGGTGAAGAAGCCTGGGGCCTCAGTGAAGGTCTCCTGCAAGGCTTCTGGATACACCTTCACCGGCTACTATATGCACTGGGTGCGACAGGCCCCTGGACAAGGGCTTGAGTGGATGGGATGGATCAACCCTAACAGTGGTGGCACAAACTATGCACAGAAGTTTCAGGGCAGGGTCACCATGACCAGGGACACGTCCATCAGCACAGCCTACATGGAGCTGAGCAGGCTGAGATCTGACGACACGGCCGTGTATTACTGTGCGAGAGA", "IGHV2-5*02": "CAGATCACCTTGAAGGAGTCTGGTCCTACGCTGGTGAAACCCACACAGACCCTCACGCTGACCTGCACCTTCTCTGGGTTCTCACTCAGCACTAGTGGAGTGGGTGTGGGCTGGATCCGTCAGCCCCCAGGAAAGGCCCTGGAGTGGCTTGCACTCATTTATTGGGATGATGATAAGCGCTACAGCCCATCTCTGAAGAGCAGGCTCACCATCACCAAGGACACCTCCAAAAACCAGGTGGTCCTTACAATGACCAACATGGACCCTGTGGACACAGCCACATATTACTGTGCACACAGAC", "IGHV2-70D*04": "CAGGTCACCTTGAAGGAGTCTGGTCCTGCGCTGGTGAAACCCACACAGACCCTCACACTGACCTGCACCTTCTCTGGGTTCTCACTCAGCACTAGTGGAATGCGTGTGAGCTGGATCCGTCAGCCCCCAGGGAAGGCCCTGGAGTGGCTTGCACGCATTGATTGGGATGATGATAAATTCTACAGCACATCTCTGAAGACCAGGCTCACCATCTCCAAGGACACCTCCAAAAACCAGGTGGTCCTTACAATGACCAACATGGACCCTGTGGACACAGCCACGTATTACTGTGCACGGATAC", "IGHV3-11*04": "CAGGTGCAGCTGGTGGAGTCTGGGGGAGGCTTGGTCAAGCCTGGAGGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCTTCAGTGACTACTACATGAGCTGGATCCGCCAGGCTCCAGGGAAGGGGCTGGAGTGGGTTTCATACATTAGTAGTAGTGGTAGTACCATATACTACGCAGACTCTGTGAAGGGCCGATTCACCATCTCCAGGGACAACGCCAAGAACTCACTGTATCTGCAAATGAACAGCCTGAGAGCCGAGGACACGGCTGTGTATTACTGTGCGAGAGA", "IGHV3-23*01": "GAGGTGCAGCTGTTGGAGTCTGGGGGAGGCTTGGTACAGCCTGGGGGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCTTTAGCAGCTATGCCATGAGCTGGGTCCGCCAGGCTCCAGGGAAGGGGCTGGAGTGGGTCTCAGCTATTAGTGGTAGTGGTGGTAGCACATACTACGCAGACTCCGTGAAGGGCCGGTTCACCATCTCCAGAGACAATTCCAAGAACACGCTGTATCTGCAAATGAACAGCCTGAGAGCCGAGGACACGGCCGTATATTACTGTGCGAAAGA", "IGHV3-66*02": "GAGGTGCAGCTGGTGGAGTCTGGGGGAGGCTTGGTCCAGCCTGGGGGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCGTCAGTAGCAACTACATGAGCTGGGTCCGCCAGGCTCCAGGGAAGGGGCTGGAGTGGGTCTCAGTTATTTATAGCGGTGGTAGCACATACTACGCAGACTCCGTGAAGGGCCGATTCACCATCTCCAGAGACAATTCCAAGAACACGCTGTATCTTCAAATGAACAGCCTGAGAGCTGAGGACACGGCTGTGTATTACTGTGCGAGAGA", "IGHV3-69-1*02": "GAGGTGCAGCTGGTGGAGTCTGGGGGAGGCTTGGTAAAGCCTGGGGGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCTTCAGTGACTACTACATGAACTGGGTCCGCCAGGCTCCAGGGAAGGGGCTGGAGTGGGTCTCATCCATTAGTAGTAGTAGTACCATATACTACGCAGACTCTGTGAAGGGCCGATTCACCATCTCCAGAGACAACGCCAAGAACTCACTGTATCTGCAAATGAACAGCCTGAGAGCCGAGGACACGGCTGTTTATTACTGTGCGAGAGA", "IGHV3-7*05": "GAGGTGCAGCTGGTGGAGTCTGGGGGAGGCTTGGTCCAGCCTGGGGGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCTTTAGTAGCTATTGGATGAGCTGGGTCCGCCAGGCTCCAGGGAAAGGGCTGGAGTGGGTGGCCAACATAAAGCAAGATGGAAGTGAGAAATACTATGTGGACTCTGTGAAGGGCCGATTCACCATCTCCAGAGACAACGCCAAGAACTCACTGTATCTGCAAATGAACAGCCTGAGAGCCGAGGACACGGCCGTGTATTACTGTGCGAGAGA", "IGHV3-9*02": "GAAGTGCAGCTGGTGGAGTCTGGGGGAGGCTTGGTACAGCCTGGCAGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCTCTGATGATTATGCCATGCACTGGGTCCGGCAAGCTCCAGGGAAGGGCCTGGAGTGGGTCTCAGGTATTAGTTGGAATAGTGGTAGCATAGGCTATGCGGACTCTGTGAAGGGCCGATTCACCATCTCCAGAGACAACGCCAAGAACTCCCTGTATCTGCAAATGAACAGTCTGAGAGCTGAGGACACGGCCTTGTATTACTGTGCAAAAGATA", "IGHV4-34*01": "CAGGTGCAGCTACAGCAGTGGGGCGCAGGACTGTTGAAGCCTTCGGAGACCCTGTCCCTCACCTGCGCTGTCTATGGTGGGTCCTTCAGTGGTTACTACTGGAGCTGGATCCGCCAGCCCCCAGGGAAGGGGCTGGAGTGGATTGGGGAAATCAATCATAGTGGAAGCACCAACTACAACCCGTCCCTCAAGAGTCGAGTCACCATATCAGTAGACACGTCCAAGAACCAGTTCTCCCTGAAGCTGAGCTCTGTGACCGCCGCGGACACGGCTGTGTATTACTGTGCGAGAGG", "IGHV4-39*09": "CAGCTGCAGCTGCAGGAGTCGGGCCCAGGACTGGTGAAGCCTTCGGAGACCCTGTCCCTCACCTGCACTGTCTCTGGTGGCTCCATCAGCAGTAGTAGTTACTACTGGGGCTGGATCCGCCAGCCCCCAGGGAAGGGGCTGGAGTGGATTGGGAGTATCTATTATAGTGGGAGCACCTACTACAACCCGTCCCTCAAGAGTCGAGTCACCATATCAGTAGACACGTCCAAGAACCAGTTCTCCCTGAAGCTGAGCTCTGTGACCGCAGCGGACACGGCCGTGTATTACTGTGCGAGAGA", "IGHV4-4*09": "CAGGTGCAGCTGCAGGAGTCGGGCCCAGGACTGGTGAAGCCTTCGGAGACCCTGTCCCTCACCTGCACTGTCTCTGGTGGCTCCATCAGTAGTTACTACTGGAGCTGGATCCGGCAGCCCCCAGGGAAGGGACTGGAGTGGATTGGGTACATCTATACCAGTGGGAGCACCAACTACAACCCCTCCCTCAAGAGTCGAGTCACCATATCAGTAGACACGTCCAAGAACCAGTTCTCCCTGAAGCTGAGCTCTGTGACCGCCGCAGACACGGCCGTGTATTACTGTGCGAGAGA", "IGHV4-61*01": "CAGGTGCAGCTGCAGGAGTCGGGCCCAGGACTGGTGAAGCCTTCGGAGACCCTGTCCCTCACCTGCACTGTCTCTGGTGGCTCCGTCAGCAGTGGTAGTTACTACTGGAGCTGGATCCGGCAGCCCCCAGGGAAGGGACTGGAGTGGATTGGGTATATCTATTACAGTGGGAGCACCAACTACAACCCCTCCCTCAAGAGTCGAGTCACCATATCAGTAGACACGTCCAAGAACCAGTTCTCCCTGAAGCTGAGCTCTGTGACCGCTGCGGACACGGCCGTGTATTACTGTGCGAGAGA", "IGHV5-51*01": "GAGGTGCAGCTGGTGCAGTCTGGAGCAGAGGTGAAAAAGCCCGGGGAGTCTCTGAAGATCTCCTGTAAGGGTTCTGGATACAGCTTTACCAGCTACTGGATCGGCTGGGTGCGCCAGATGCCCGGGAAAGGCCTGGAGTGGATGGGGATCATCTATCCTGGTGACTCTGATACCAGATACAGCCCGTCCTTCCAAGGCCAGGTCACCATCTCAGCCGACAAGTCCATCAGCACCGCCTACCTGCAGTGGAGCAGCCTGAAGGCCTCGGACACCGCCATGTATTACTGTGCGAGACA"}, "d": {"IGHD1-20*01": "GGTATAACTGGAACGAC", "IGHD1-26*01": "GGTATAGTGGGAGCTACTAC", "IGHD2-15*01": "AGGATATTGTAGTGGTGGTAGCTGCTACTCC", "IGHD2-2*01": "AGGATATTGTAGTAGTACCAGCTGCTATGCC", "IGHD2-21*01": "AGCATATTGTGGTGGTGATTGCTATTCC", "IGHD2-21*02": "AGCATATTGTGGTGGTGACTGCTATTCC", "IGHD2-8*01": "AGGATATTGTACTAATGGTGTATGCTATACC", "IGHD2-8*02": "AGGATATTGTACTGGTGGTGTATGCTATACC", "IGHD3-10*01": "GTATTACTATGGTTCGGGGAGTTATTATAAC", "IGHD3-10*03": "GTATTACTATGGTTCAGGGAGTTATTATAAC", "IGHD3-16*02": "GTATTATGATTACGTTTGGGGGAGTTATCGTTATACC", "IGHD3-22*01": "GTATTACTATGATAGTAGTGGTTATTACTAC", "IGHD3-3*01": "GTATTACGATTTTTGGAGTGGTTATTATACC", "IGHD4-17*01": "TGACTACGGTGACTAC", "IGHD4-4*01": "TGACTACAGTAACTAC", "IGHD5-5*01": "GTGGATACAGCTATGGTTAC", "IGHD6-13*01": "GGGTATAGCAGCAGCTGGTAC", "IGHD6-19*01": "GGGTATAGCAGTGGCTGGTAC", "IGHD6-6*01": "GAGTATAGCAGCTCGTCC"}, "j": {"IGHJ1*01": "GCTGAATACTTCCAGCACTGGGGCCAGGGCACCCTGGTCACCGTCTCCTCAG", "IGHJ2*01": "CTACTGGTACTTCGATCTCTGGGGCCGTGGCACCCTGGTCACTGTCTCCTCAG", "IGHJ3*02": "TGATGCTTTTGATATCTGGGGCCAAGGGACAATGGTCACCGTCTCTTCAG", "IGHJ4*02": "ACTACTTTGACTACTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG", "IGHJ5*02": "ACAACTGGTTCGACCCCTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG", "IGHJ6*02": "ATTACTACTACTACTACGGTATGGACGTCTGGGGCCAAGGGACCACGGTCACCGTCTCCTCAG", "IGHJ6*03": "ATTACTACTACTACTACTACATGGACGTCTGGGGCAAAGGGACCACGGTCACCGTCTCCTCAG"}}, "cyst-positions": {"IGHV2-5*02": 288, "IGHV4-34*01": 282, "IGHV1-2*02": 285, "IGHV1-18*01": 285, "IGHV3-7*05": 285, "IGHV3-69-1*02": 282, "IGHV3-11*04": 285, "IGHV2-70D*04": 288, "IGHV5-51*01": 285, "IGHV3-66*02": 282, "IGHV4-39*09": 288, "IGHV3-9*02": 285, "IGHV3-23*01": 285, "IGHV4-61*01": 288, "IGHV4-4*09": 282}, "tryp-positions": {"IGHJ4*02": 14, "IGHJ2*01": 19, "IGHJ3*02": 16, "IGHJ6*02": 29, "IGHJ5*02": 17, "IGHJ1*01": 18, "IGHJ6*03": 29}}, "partitions": [{"logprob": 0.0, "n_clusters": 10, "n_procs": 1, "partition": [["fc846a4540", "f977acb49b", "9a4254e968"], ["e883678985", "d3487934e0", "2ded5892c4", "2ed5fb6457", "19458e6805", "0ee3136ea7", "279a8071f5", "e004ac921a", "ec4aa1d63b"], ["52a4cc50e5"], ["081307416c", "91796617a0", "4233d708fe", "a484f584e9", "13de8675ec", "33aaa62e12", "31e052ee14"], ["226be79d5f", "188e1a0235"], ["eeca70ed28", "c7a8a5b2f0", "b2982a29ea", "d9172b4f22", "27eccd7baf", "21f0e10a44", "64de54c978", "579bc5aa80"], ["f29bce4695", "36d80d25ae"], ["d024e5cab0", "822801f8ab"], ["c19efdaf0d"], ["5f7b69c48f"]]}], "events": [{"qr_gap_seqs": ["", "", ""], "gl_gap_seqs": ["", "", ""], "indel_reversed_seqs": ["", "", ""], "reco_id": "5611db2b0a", "tree": "[&R] (((fc846a4540:0.011735241311499707,f977acb49b:0.011735241311499707)fhu:0.000596485808076228,9a4254e968:0.012331727121575934)fty:0.006419249533820349)ael:0.0;\n", "unique_ids": ["fc846a4540", "f977acb49b", "9a4254e968"], "invalid": false, "v_gene": "IGHV3-7*05", "d_gene": "IGHD6-13*01", "j_gene": "IGHJ6*02", "cdr3_length": 63, "mut_freqs": [0.026385224274406333, 0.023746701846965697, 0.021108179419525065], "n_mutations": [10, 9, 8], "input_seqs": ["GAGGTGCAGCTGGTGGAGTCTGGGGGAGGCTTGGTCCAGCCTGGGGGGTCCCTGAGACTCTCCTGTGCAGCCTCTTGATTCACCTTTAGTAGCTATTGGATGAGCTGGGTCCGCCAGGCTCCAGGGAAAAGGCTGGAGTGGGTGGCCAACATAAAGCAAGATGGAAGTGAGAAATACTATGTGGACTCTGTAAAGGGCCGATTCACCATCTCCAGGGACAACGCCAAGAACTCACTGTATCTGCAGATGAACAGCCTGAGAGCCGTGGACACGGCCGTGTATTACTGTGCGAGAGACTGCGAAGTAGCTGGTACCTATTGTAAGTTACGTGAGGGTATGGACGTCTGGGGCCAAGGGAACACGGTCACCGTCTCCTCAG", "GAGGTGCACCTGGTGGAGTCTGGGGGAGGCTTGGTCCAGCCTGGGGGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCTTTAGTAGCTATTGAATGAGCTGGGTCCGCCAGGCTCCAGGGAAAAGGCTGGAGTGGGTGGCCAACATAAAGCAAGATGGAAATGAGAAATACTATGTGGACTCTATGAAGGGCCGATTCACCATCTCCAGAGACAACGCCAAGAACTCACTGTATCTGCAGATGAACAGCTTGAGAGCCGAGGACACGGCCGTGTATTACTGTGCGAGAGACTGCGAAGCAGCTGGTACCTATTGTAACTTGCGTGAGGGTATGGACGTCTGGGGCCAAGGGACCACGGTCACCGTCTCCTCAG", "GAGGTGCAGCTGGTGGAGTCTGGGGGAGGCCTGGTCCAGCCTGGGGGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCATCTTTAGTAGCTATTGGATGAGCTGGGTCCGCCAGGCTCCAGGGAAAAGGCTGGAGTGGGTGGCCAACATAAAGCAAGATGGAAGTGAGAAATACTATGTGGACTCTGTGGAGGGCCGATTCACCATCTCCAGAGACAACGCCAAGAACTCACTGTATCTGCAGATGAACAGCCTGAGAGCCGAGGACACGGCCGTGTACTACTGTGCGAGAGACTGCGAAGCAGGTGGTACCTATTGTAAGTTGCGTGAGGGTATGGACGTCTGGGGCCAAGGGACCACGGTCACCGTCTCCTCAG"], "has_shm_indels": [false, false, false], "naive_seq": "GAGGTGCAGCTGGTGGAGTCTGGGGGAGGCTTGGTCCAGCCTGGGGGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCTTTAGTAGCTATTGGATGAGCTGGGTCCGCCAGGCTCCAGGGAAAGGGCTGGAGTGGGTGGCCAACATAAAGCAAGATGGAAGTGAGAAATACTATGTGGACTCTGTGAAGGGCCGATTCACCATCTCCAGAGACAACGCCAAGAACTCACTGTATCTGCAAATGAACAGCCTGAGAGCCGAGGACACGGCCGTGTATTACTGTGCGAGAGACTGCGAAGCAGCTGGTACCTATTCTAAGTTGCGTGAGGGTATGGACGTCTGGGGCCAAGGGACCACGGTCACCGTCTCCTCAG", "duplicates": [[], [], []], "v_3p_del": 0, "d_5p_del": 9, "d_3p_del": 0, "j_5p_del": 17, "v_5p_del": 0, "j_3p_del": 0, "vd_insertion": "CTGCGA", "dj_insertion": "CTATTCTAAGTTGCGTGAG", "fv_insertion": "", "jf_insertion": "", "mutated_invariants": [false, false, false], "in_frames": [true, true, true], "stops": [true, true, false], "loci": ["igh", "igh", "igh"], "codon_positions": {"v": 285, "j": 345}}, {"qr_gap_seqs": ["", "", "", "", "", "", "", "", ""], "gl_gap_seqs": ["", "", "", "", "", "", "", "", ""], "indel_reversed_seqs": ["", "", "", "", "", "", "", "", ""], "reco_id": "fbdf4feea6", "tree": "[&R] (((19458e6805:0.015182952109610126,((ec4aa1d63b:0.012757629919672404,(279a8071f5:0.0002717575583930217,(e004ac921a:0.0001314647675966242,e883678985:0.0001314647675966242)cpu:0.00014029279079639753)cqx:0.012485872369679383)aru:0.002397661445938432,2ed5fb6457:0.015155291369610838)lqs:2.766074313928972e-05)fhp:0.002232979424942661,(d3487934e0:0.01469171558962274,(0ee3136ea7:0.0051119153638687345,2ded5892c4:0.0051119153638687345)duw:0.009579800227754006)irt:0.002724215945930047)pqz:0.0013350451159657181)ahx:0.0;\n", "unique_ids": ["e883678985", "d3487934e0", "2ded5892c4", "2ed5fb6457", "19458e6805", "0ee3136ea7", "279a8071f5", "e004ac921a", "ec4aa1d63b"], "invalid": false, "v_gene": "IGHV3-66*02", "d_gene": "IGHD6-13*01", "j_gene": "IGHJ4*02", "cdr3_length": 33, "mut_freqs": [0.002890173410404624, 0.023121387283236993, 0.017341040462427744, 0.017341040462427744, 0.014450867052023121, 0.02601156069364162, 0.002890173410404624, 0.002890173410404624, 0.008670520231213872], "n_mutations": [1, 8, 6, 6, 5, 9, 1, 1, 3], "input_seqs": ["GAGGTGCAGCTGGTGGAGTCTGGGGGAGGCTTGGTCCAGCCTGGGGGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCGTCAGTAGCAACTACATGAGCTGGGTCCGCCAGGCTCCAGGGAAGGGGCTGGAGTGGGTCTCAGTTATTTATAGCGGTGGTAGCACATACTACGCAGACTCCGTGAAGGGCCGATTCACCATCTCCAGAGACAATTCCAAGAACACGCTGTATCTTCAAATGAACAGCCTGAGAGCTGAGGACACGGCTGTGTATTACTGTGCGAGATCCATAGCAGCAGCCGACTACTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG", "GAGGTGCAGCTGGTGGAGTCTGGGGGAGGCCTGGTCCAGCCTGGGGGGTCTCTGAGACTCTCCTGTGCAGCGTCTGGATTCACCGTCAGTAGCAACTACATGAGCTGGGTCCGCCAGGCTCCAGGGAAGGGGCTGGAGTGGGTGTCAGTTATTTATAGCGGTGGTAGCACATACTACGCAGACTTCGTGAAGGGCCGATTGACCATCTCCAGAGACAATTCCAAGAACACGCTGTATCTTCAAATGAACAGCCTGAGTGCTGAGGACACGGCTGTGTATTACTGTGCGAGATCTATAGCAGCAGCCGACTACTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAA", "GAGGTGCAGCTGGTGGAGTCTGGGGGAGGCTTGGTCCAGCCTGGGGGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTTACCGTCAGTAGCAACTACATGAGCTGGGTCCGCCAGGCTCCAGGGAAGGGGCTGGAGTGGGTCTCAGTTATTTATTGCGGTGGTAGCACATACTACGCAGACTCCGTGAAGGGCCGATTCACCATCTCCAGAGACAATTCCAAGAACACGGTGTATCTTCAAATGAACAGCCTGAGAGCTGAGGACACGGCTGTGTATTACTGTGCGAGATCTATAGCAGCAGCCGACTACTGGGGCTAGGGATCCCTGGTCACCGTCTCCTCAA", "GAGGTGCAGCTGGTGGAGTCTGGAGGAGGCTTGGTCCAGCCTGGAGGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCGCCAGTAGCAACTACATGAGCTGGGTCCGCCAGGCTCCAGGGAAGGGGCTGGAGTGGGTCTCAGTTATTTAAAGCGGTGGTAGCACATACTACGCAGACTCCGTGAAGGGCCGATTCACCACCTCCAGAGACAATTCCAAGAACACGCTGTATCTTCAAATGAACAGCCTGAGAGCTGAGGACACGGCAGTGTATTACTGTGCGAGATCTATAGCAGCAGCCGACTACTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG", "GAGGTGCAGCTGGTGGAGTCTGGGGGAGACTTGGTCCAGCCTGGGGGGTCCCTGAGACTCTCCTGTCCAGCCTCTCGATTCACCGTCAGTAGCAACTACATGAGCTGGGTCCGCCAGGCTCCAGGGAAGGGGCTGGAGTGGGTCTCAGTTATTTATAGCGGTGGTAGCACATACTACGCAGACTCCGTGAAGGGCCGATTCACCATCTCCAGAGACAATTCCAAGAACACGCTATATCTTCAAATGAACAGCCTGAGAGCTGAGGACACGGCTGTGTATTACTGTACGAGATCTATAGCAGCAGCCGACTACTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG", "TAGGTGCAGCTGGTGGAGTCTGGGGGAGGCTTGGTCCAGCCTGGGGGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTTACCGTCAGTAGCAACTATATGAGCTGGGTCCGCCAGGCTCCAGGGAAGGGGCTGGAGTGGGTCTCAGTTATTTATTGCGGTGGTAGCACATACTACGCAGACTCCGTGAAGGGCCGATTCACCATCTCCAGAGCCAATTCCAAGAACACGCTGTATCTTCAAATGAACAGCCTGAGAGCTGAGGACACGGCTGTGTATTACTGTGCGAGATCTATAGCAGCAGCCCACTACTGGGGCTAGGGATCCCTGGTCACCGTCTCCTCAA", "GAGGTGCAGCTGGTGGAGTCTGGGGGAGGCTTGGTCCAGCCTGGGGGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCGTCAGTAGCAACTACATGAGCTGGGTCCGCCAGGCTCCAGGGAAGGGGCTGGAGTGGGTCTCAGTTATTTATAGCGGTGGTAGCACATACTACGCAGACTCCGTGAAGGGCCGATTCACCATCTCCAGAGACAATTCCAAGAACACGCTGTATCTTCAAATGAACAGCCTGAGAGCTGAGGACACGGCTGTGTATTACTGTGCGAGATCCATAGCAGCAGCCGACTACTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG", "GAGGTGCAGCTGGTGGAGTCTGGGGGAGGCTTGGTCCAGCCTGGGGGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCGTCAGTAGCAACTACATGAGCTGGGTCCGCCAGGCTCCAGGGAAGGGGCTGGAGTGGGTCTCAGTTATTTATAGCGGTGGTAGCACATACTACGCAGACTCCGTGAAGGGCCGATTCACCATCTCCAGAGACAATTCCAAGAACACGCTGTATCTTCAAATGAACAGCCTGAGAGCTGAGGACACGGCTGTGTATTACTGTGCGAGATCCATAGCAGCAGCCGACTACTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG", "GAGGTGCAGCTGGTGGAGTCTGGGGGAGGCTTGGTCCAGCTTGGGGGGTCCCTGAGACTCTCCTGTGCAGCCTCTAGATTCACCGTCAGTAGCAACTACATGAGCTGGGTCCGCCAGGCTCCAGGGAAGGGGCTGGAGTGGGTCTCAGTTATTTATAGCGGTGGTAGCACATACTACGCAGACTCTGTGAAGGGCCGATTCACCATCTCCAGAGACAATTCCAAGAACACGCTGTATCTTCAAATGAACAGCCTGAGAGCTGAGGACACGGCTGTGTATTACTGTGCGAGATCTATAGCAGCAGCCGACTACTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG"], "has_shm_indels": [false, false, false, false, false, false, false, false, false], "naive_seq": "GAGGTGCAGCTGGTGGAGTCTGGGGGAGGCTTGGTCCAGCCTGGGGGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCGTCAGTAGCAACTACATGAGCTGGGTCCGCCAGGCTCCAGGGAAGGGGCTGGAGTGGGTCTCAGTTATTTATAGCGGTGGTAGCACATACTACGCAGACTCCGTGAAGGGCCGATTCACCATCTCCAGAGACAATTCCAAGAACACGCTGTATCTTCAAATGAACAGCCTGAGAGCTGAGGACACGGCTGTGTATTACTGTGCGAGATCTATAGCAGCAGCCGACTACTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG", "duplicates": [[], [], [], [], [], [], [], [], []], "v_3p_del": 2, "d_5p_del": 3, "d_3p_del": 6, "j_5p_del": 8, "v_5p_del": 0, "j_3p_del": 0, "vd_insertion": "TC", "dj_insertion": "C", "fv_insertion": "", "jf_insertion": "", "mutated_invariants": [false, false, false, false, false, false, false, false, false], "in_frames": [true, true, true, true, true, true, true, true, true], "stops": [false, false, true, true, false, true, false, false, false], "loci": ["igh", "igh", "igh", "igh", "igh", "igh", "igh", "igh", "igh"], "codon_positions": {"v": 282, "j": 312}}, {"qr_gap_seqs": [""], "gl_gap_seqs": [""], "indel_reversed_seqs": [""], "reco_id": "a5090d8abc", "tree": "[&R] (52a4cc50e5:0.013345547850351035)cqu:0.0;\n", "unique_ids": ["52a4cc50e5"], "invalid": false, "v_gene": "IGHV4-4*09", "d_gene": "IGHD6-13*01", "j_gene": "IGHJ4*02", "cdr3_length": 48, "mut_freqs": [0.027700831024930747], "n_mutations": [10], "input_seqs": ["CAAGTGCAACTGCAGGAGTCGGGCCGAGGACTGGTGAAGCCTTCGGAGACCCTGTCCCTCACCTGCACTGTCTCTGGTGGCTCCATCAGTAGTTACTACTGGAGCTAGATCCGGCAGCCCCCAGGGAAGGGACTGGAGTGGATTGGGTACCTCTATACCAGTGGGAGCACCAACTACAACCCCTCCCTCAAGAGTCGAGTCACCATATCAGTAGACACGTCCAAGAACCAGTTCTCCCTGAAACTGAGCTCTGTGACCGCCGCAGACACGGCCATATATTACTGTGCGAGTTATTTGCTCGGGTACAGCAGCAGAGCCCCTGTCTACTGGGGCCAGCGAACCCTGGTCACCGTCTCCTCAG"], "has_shm_indels": [false], "naive_seq": "CAGGTGCAGCTGCAGGAGTCGGGCCCAGGACTGGTGAAGCCTTCGGAGACCCTGTCCCTCACCTGCACTGTCTCTGGTGGCTCCATCAGTAGTTACTACTGGAGCTGGATCCGGCAGCCCCCAGGGAAGGGACTGGAGTGGATTGGGTACATCTATACCAGTGGGAGCACCAACTACAACCCCTCCCTCAAGAGTCGAGTCACCATATCAGTAGACACGTCCAAGAACCAGTTCTCCCTGAAGCTGAGCTCTGTGACCGCCGCAGACACGGCCGTGTATTACTGTGCGAGTTATTTGCTCGGGTATAGCAGCAGAGCCCCTGTCTACTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG", "duplicates": [[]], "v_3p_del": 3, "d_5p_del": 0, "d_3p_del": 7, "j_5p_del": 10, "v_5p_del": 0, "j_3p_del": 0, "vd_insertion": "TTATTTGCTC", "dj_insertion": "AGCCCCTGT", "fv_insertion": "", "jf_insertion": "", "mutated_invariants": [false], "in_frames": [true], "stops": [true], "loci": ["igh"], "codon_positions": {"v": 282, "j": 327}}, {"qr_gap_seqs": ["", "", "", "", "", "CAGGTTCAGCTGGTGCAGTCTGGAGCTGAGGTGAAGAAGCCTGGGGCCTCAGTGAAGGTCTCCTGCAAGGCTTCTGGTTACACCTTTACCAGCTATGGTATCAGCTGGGTGCGACAGGCCCCTGGACAAGGGCTTGAGTGGATGGGATGGATCAGCGCTTACAATGGTAACACAAACTATGCACAGAAGCTCCAGGGCAGAGTCACCATGACCACAGACACATCCACGAGCACAGCCTACATGGAGCTAAGCTGTGAGGAGCCTGAGATCTGACGACACGGCCGTGTATTACTGTGCGAGAGACCCCTCGCAGTATAGCAGCAGCTTCCCTTTTGACTACTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG", "CAGGTTCAGCTGGTGCAGTCTGGAGCTGAGGTGAAGAAGCCTGGGGCCTCAGTGAAGGTCTCCTGCAAGGGACCTTCTGGTTACACCTTTACCAGCTATGGTATCAGCTGGGTGCGACAGGCCCCTGGACAAGGGCTTGAGTGGATGGGATGGATCAGCGCTTACAATGGTAACACAAACTATGCACAGAAGCTCCAGGGCAGAGTCACCATGACCACAGACACATCCACGAGCACAGCCTACATGGAGCTGAGGAGCCTGAGATCTGACGACACGGCCGTGTATTACTGTGCGAGAGACCCCTCGCAGTATAGCAGCAGCTTCCCTTTTGACTACTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG"], "gl_gap_seqs": ["", "", "", "", "", "CAGGTTCAGCTGGTGCAGTCTGGAGCTGAGGTGAAGAAGCCTGGGGCCTCAGTGAAGGTCTCCTGCAAGGCTTCTGGTTACACCTTTACCAGCTATGGTATCAGCTGGGTGCGACAGGCCCCTGGACAAGGGCTTGAGTGGATGGGATGGATCAGCGCTTACAATGGTAACACAAACTATGCACAGAAGCTCCAGGGCAGAGTCACCATGACCACAGACACATCCACGAGCACAGCCTACATGGAGCT.......GAGGAGCCTGAGATCTGACGACACGGCCGTGTATTACTGTGCGAGAGACCCCTCGCAGTATAGCAGCAGCTTCCCTTTTGACTACTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG", "CAGGTTCAGCTGGTGCAGTCTGGAGCTGAGGTGAAGAAGCCTGGGGCCTCAGTGAAGGTCTCCTGCAAGG...CTTCTGGTTACACCTTTACCAGCTATGGTATCAGCTGGGTGCGACAGGCCCCTGGACAAGGGCTTGAGTGGATGGGATGGATCAGCGCTTACAATGGTAACACAAACTATGCACAGAAGCTCCAGGGCAGAGTCACCATGACCACAGACACATCCACGAGCACAGCCTACATGGAGCTGAGGAGCCTGAGATCTGACGACACGGCCGTGTATTACTGTGCGAGAGACCCCTCGCAGTATAGCAGCAGCTTCCCTTTTGACTACTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG"], "indel_reversed_seqs": ["", "", "", "", "", "CAGGTTCAGCTGGTGCAGTCTGGAGCTGAGGTGAAGAAGCCTGGGGCCTCAGTGAAGGTCTCCTGCAAGGCTTCTGGTTACACCTTTACCAGCTATGGTATCAGCTGGGTGCGACAGGCCCCTGGACAAGGGCTTGAGTGGATGGGATGGATCAGCGCTTACAATGGTAACACAAACTATGCACAGAAGCTCCAGGGCAGAGTCACCATGACCACAGACACATCCACGAGCACAGCCTACATGGAGCTGAGGAGCCTGAGATCTGACGACACGGCCGTGTATTACTGTGCGAGAGACCCCTCGCAGTATAGCAGCAGCTTCCCTTTTGACTACTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG", "CAGGTTCAGCTGGTGCAGTCTGGAGCTGAGGTGAAGAAGCCTGGGGCCTCAGTGAAGGTCTCCTGCAAGGCTTCTGGTTACACCTTTACCAGCTATGGTATCAGCTGGGTGCGACAGGCCCCTGGACAAGGGCTTGAGTGGATGGGATGGATCAGCGCTTACAATGGTAACACAAACTATGCACAGAAGCTCCAGGGCAGAGTCACCATGACCACAGACACATCCACGAGCACAGCCTACATGGAGCTGAGGAGCCTGAGATCTGACGACACGGCCGTGTATTACTGTGCGAGAGACCCCTCGCAGTATAGCAGCAGCTTCCCTTTTGACTACTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG"], "reco_id": "9dacfa8deb", "tree": "[&R] ((081307416c:0.002623905430250834,(((33aaa62e12:0.0018644309441782313,(4233d708fe:0.0007456991718712855,91796617a0:0.0007456991718712855)bcq:0.0011187317721069456)cgu:0.0003440212853328869,a484f584e9:0.002208452229211118)dtz:0.0002014382533192566,(13de8675ec:0.0006150090664587922,31e052ee14:0.0006150090664587922)hty:0.0017948814161715826)bik:0.00021401494702045888)kqu:2.6274006232511675e-05)evz:0.0;\n", "unique_ids": ["081307416c", "91796617a0", "4233d708fe", "a484f584e9", "13de8675ec", "33aaa62e12", "31e052ee14"], "invalid": false, "v_gene": "IGHV1-18*01", "d_gene": "IGHD6-13*01", "j_gene": "IGHJ4*02", "cdr3_length": 51, "mut_freqs": [0.008174386920980926, 0.0, 0.0, 0.0027247956403269754, 0.0, 0.0, 0.0], "n_mutations": [3, 0, 0, 1, 0, 0, 0], "input_seqs": ["CAGGTTCAGCTGGTGCAATCTGGAGCTGAGGTGTAGAAGCTTGGGGCCTCAGTGAAGGTCTCCTGCAAGGCTTCTGGTTACACCTTTACCAGCTATGGTATCAGCTGGGTGCGACAGGCCCCTGGACAAGGGCTTGAGTGGATGGGATGGATCAGCGCTTACAATGGTAACACAAACTATGCACAGAAGCTCCAGGGCAGAGTCACCATGACCACAGACACATCCACGAGCACAGCCTACATGGAGCTGAGGAGCCTGAGATCTGACGACACGGCCGTGTATTACTGTGCGAGAGACCCCTCGCAGTATAGCAGCAGCTTCCCTTTTGACTACTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG", "CAGGTTCAGCTGGTGCAGTCTGGAGCTGAGGTGAAGAAGCCTGGGGCCTCAGTGAAGGTCTCCTGCAAGGCTTCTGGTTACACCTTTACCAGCTATGGTATCAGCTGGGTGCGACAGGCCCCTGGACAAGGGCTTGAGTGGATGGGATGGATCAGCGCTTACAATGGTAACACAAACTATGCACAGAAGCTCCAGGGCAGAGTCACCATGACCACAGACACATCCACGAGCACAGCCTACATGGAGCTGAGGAGCCTGAGATCTGACGACACGGCCGTGTATTACTGTGCGAGAGACCCCTCGCAGTATAGCAGCAGCTTCCCTTTTGACTACTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG", "CAGGTTCAGCTGGTGCAGTCTGGAGCTGAGGTGAAGAAGCCTGGGGCCTCAGTGAAGGTCTCCTGCAAGGCTTCTGGTTACACCTTTACCAGCTATGGTATCAGCTGGGTGCGACAGGCCCCTGGACAAGGGCTTGAGTGGATGGGATGGATCAGCGCTTACAATGGTAACACAAACTATGCACAGAAGCTCCAGGGCAGAGTCACCATGACCACAGACACATCCACGAGCACAGCCTACATGGAGCTGAGGAGCCTGAGATCTGACGACACGGCCGTGTATTACTGTGCGAGAGACCCCTCGCAGTATAGCAGCAGCTTCCCTTTTGACTACTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG", "CAGGTTCAGCTGGTGCAGTCTGGAGCTGAGGTGAACAAGCCTGGGGCCTCAGTGAAGGTCTCCTGCAAGGCTTCTGGTTACACCTTTACCAGCTATGGTATCAGCTGGGTGCGACAGGCCCCTGGACAAGGGCTTGAGTGGATGGGATGGATCAGCGCTTACAATGGTAACACAAACTATGCACAGAAGCTCCAGGGCAGAGTCACCATGACCACAGACACATCCACGAGCACAGCCTACATGGAGCTGAGGAGCCTGAGATCTGACGACACGGCCGTGTATTACTGTGCGAGAGACCCCTCGCAGTATAGCAGCAGCTTCCCTTTTGACTACTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG", "CAGGTTCAGCTGGTGCAGTCTGGAGCTGAGGTGAAGAAGCCTGGGGCCTCAGTGAAGGTCTCCTGCAAGGCTTCTGGTTACACCTTTACCAGCTATGGTATCAGCTGGGTGCGACAGGCCCCTGGACAAGGGCTTGAGTGGATGGGATGGATCAGCGCTTACAATGGTAACACAAACTATGCACAGAAGCTCCAGGGCAGAGTCACCATGACCACAGACACATCCACGAGCACAGCCTACATGGAGCTGAGGAGCCTGAGATCTGACGACACGGCCGTGTATTACTGTGCGAGAGACCCCTCGCAGTATAGCAGCAGCTTCCCTTTTGACTACTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG", "CAGGTTCAGCTGGTGCAGTCTGGAGCTGAGGTGAAGAAGCCTGGGGCCTCAGTGAAGGTCTCCTGCAAGGCTTCTGGTTACACCTTTACCAGCTATGGTATCAGCTGGGTGCGACAGGCCCCTGGACAAGGGCTTGAGTGGATGGGATGGATCAGCGCTTACAATGGTAACACAAACTATGCACAGAAGCTCCAGGGCAGAGTCACCATGACCACAGACACATCCACGAGCACAGCCTACATGGAGCTAAGCTGTGAGGAGCCTGAGATCTGACGACACGGCCGTGTATTACTGTGCGAGAGACCCCTCGCAGTATAGCAGCAGCTTCCCTTTTGACTACTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG", "CAGGTTCAGCTGGTGCAGTCTGGAGCTGAGGTGAAGAAGCCTGGGGCCTCAGTGAAGGTCTCCTGCAAGGGACCTTCTGGTTACACCTTTACCAGCTATGGTATCAGCTGGGTGCGACAGGCCCCTGGACAAGGGCTTGAGTGGATGGGATGGATCAGCGCTTACAATGGTAACACAAACTATGCACAGAAGCTCCAGGGCAGAGTCACCATGACCACAGACACATCCACGAGCACAGCCTACATGGAGCTGAGGAGCCTGAGATCTGACGACACGGCCGTGTATTACTGTGCGAGAGACCCCTCGCAGTATAGCAGCAGCTTCCCTTTTGACTACTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG"], "has_shm_indels": [false, false, false, false, false, true, true], "naive_seq": "CAGGTTCAGCTGGTGCAGTCTGGAGCTGAGGTGAAGAAGCCTGGGGCCTCAGTGAAGGTCTCCTGCAAGGCTTCTGGTTACACCTTTACCAGCTATGGTATCAGCTGGGTGCGACAGGCCCCTGGACAAGGGCTTGAGTGGATGGGATGGATCAGCGCTTACAATGGTAACACAAACTATGCACAGAAGCTCCAGGGCAGAGTCACCATGACCACAGACACATCCACGAGCACAGCCTACATGGAGCTGAGGAGCCTGAGATCTGACGACACGGCCGTGTATTACTGTGCGAGAGACCCCTCGCAGTATAGCAGCAGCTTCCCTTTTGACTACTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG", "duplicates": [[], [], [], [], [], [], []], "v_3p_del": 0, "d_5p_del": 2, "d_3p_del": 7, "j_5p_del": 6, "v_5p_del": 0, "j_3p_del": 0, "vd_insertion": "CCCCTCGCA", "dj_insertion": "CTTCCCTT", "fv_insertion": "", "jf_insertion": "", "mutated_invariants": [false, false, false, false, false, false, false], "in_frames": [true, true, true, true, true, false, true], "stops": [true, false, false, false, false, true, false], "loci": ["igh", "igh", "igh", "igh", "igh", "igh", "igh"], "codon_positions": {"v": 285, "j": 333}}, {"qr_gap_seqs": ["", ""], "gl_gap_seqs": ["", ""], "indel_reversed_seqs": ["", ""], "reco_id": "f220c52535", "tree": "[&R] ((226be79d5f:0.001583152227990051,188e1a0235:0.001583152227990051)hmq:0.0010670272079932946)afh:0.0;\n", "unique_ids": ["226be79d5f", "188e1a0235"], "invalid": false, "v_gene": "IGHV3-23*01", "d_gene": "IGHD3-16*02", "j_gene": "IGHJ4*02", "cdr3_length": 54, "mut_freqs": [0.0, 0.0], "n_mutations": [0, 0], "input_seqs": ["GAGGTGCAGCTGTTGGAGTCTGGGGGAGGCTTGGTACAGCCTGGGGGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCTTTAGCAGCTATGCCATGAGCTGGGTCCGCCAGGCTCCAGGGAAGGGGCTGGAGTGGGTCTCAGCTATTAGTGGTAGTGGTGGTAGCACATACTACGCAGACTCCGTGAAGGGCCGGTTCACCATCTCCAGAGACAATTCCAAGAACACGCTGTATCTGCAAATGAACAGCCTGAGAGCCGAGGACACGGCCGTATATTACTGTGCGAAAGAATTACGTTTGGGGGAGTTATCGTTATACCCCTTTGACTACTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG", "GAGGTGCAGCTGTTGGAGTCTGGGGGAGGCTTGGTACAGCCTGGGGGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCTTTAGCAGCTATGCCATGAGCTGGGTCCGCCAGGCTCCAGGGAAGGGGCTGGAGTGGGTCTCAGCTATTAGTGGTAGTGGTGGTAGCACATACTACGCAGACTCCGTGAAGGGCCGGTTCACCATCTCCAGAGACAATTCCAAGAACACGCTGTATCTGCAAATGAACAGCCTGAGAGCCGAGGACACGGCCGTATATTACTGTGCGAAAGAATTACGTTTGGGGGAGTTATCGTTATACCCCTTTGACTACTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG"], "has_shm_indels": [false, false], "naive_seq": "GAGGTGCAGCTGTTGGAGTCTGGGGGAGGCTTGGTACAGCCTGGGGGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCTTTAGCAGCTATGCCATGAGCTGGGTCCGCCAGGCTCCAGGGAAGGGGCTGGAGTGGGTCTCAGCTATTAGTGGTAGTGGTGGTAGCACATACTACGCAGACTCCGTGAAGGGCCGGTTCACCATCTCCAGAGACAATTCCAAGAACACGCTGTATCTGCAAATGAACAGCCTGAGAGCCGAGGACACGGCCGTATATTACTGTGCGAAAGAATTACGTTTGGGGGAGTTATCGTTATACCCCTTTGACTACTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG", "duplicates": [[], []], "v_3p_del": 0, "d_5p_del": 8, "d_3p_del": 0, "j_5p_del": 4, "v_5p_del": 0, "j_3p_del": 0, "vd_insertion": "", "dj_insertion": "C", "fv_insertion": "", "jf_insertion": "", "mutated_invariants": [false, false], "in_frames": [true, true], "stops": [false, false], "loci": ["igh", "igh"], "codon_positions": {"v": 285, "j": 336}}, {"qr_gap_seqs": ["", "CAGGTGCAGCTGCAGGAGTCGGGCCCGGGACTGGTGAAGCCTTCGGAGACCCTGT.......CTGCACTGTCTCTGGTGGCTCCGTCAGCAGTGGTAGTTACTACTGGAGCTGGATCCGGCAGCCCCCAGGGAAGGGACTGGAGTGGATTGGGTATATCTATTACAGTGGGAGCACCAACTACAACCCCTCCCTCAAGAGTCGAGTCACCATATCAGTAGACACGTCCAAAAACCAGTTCTCGCTGAAGCTGAGCTCTGTGACCGCTGCGGACACGGCCGTGTATTACTGTGCGAGAGAGTATTACTATGA.....GTGGTTATTACTACGAATACTTCCAGCATTGGGGCCAGGGCACCCTGGTCACCGTCTCCTCAG", "", "CAGGTGCAGCTGCAGGAGTCGGGTCCAGGACTGATGAAGCCTTCGGAGACCCTGTCCCTCACCTGCACTGTCTCTGGTGGCTCCGTCAGCAGTGGTAGTTACTACTGGAGCTGGATCCGGCAGCCCCCAGCGAAGGGACTGGAGTGGATTGGGTATATCTATTACAGTGGGAGCGCCAACTACAACCCCTCCCTCAAGAGTCGAGTCACCATATCAGTAGACACGTCCAAGAACCA............GCTGAGCTCTGTGACCGCTGCGGACACGGCCGTGTATTACTGTGCGAGAAAGTATTACTATGATAGTAGTGGTTATTACTACGAATACTTCATTCCAGCACTGGGGCCAGGGCACCCTGGCCACCGTCTCCTCAG", "", "", "", ""], "gl_gap_seqs": ["", "CAGGTGCAGCTGCAGGAGTCGGGCCCAGGACTGGTGAAGCCTTCGGAGACCCTGTCCCTCACCTGCACTGTCTCTGGTGGCTCCGTCAGCAGTGGTAGTTACTACTGGAGCTGGATCCGGCAGCCCCCAGGGAAGGGACTGGAGTGGATTGGGTATATCTATTACAGTGGGAGCACCAACTACAACCCCTCCCTCAAGAGTCGAGTCACCATATCAGTAGACACGTCCAAGAACCAGTTCTCCCTGAAGCTGAGCTCTGTGACCGCTGCGGACACGGCCGTGTATTACTGTGCGAGAGAGTATTACTATGATAGTAGTGGTTATTACTACGAATACTTCCAGCACTGGGGCCAGGGCACCCTGGTCACCGTCTCCTCAG", "", "CAGGTGCAGCTGCAGGAGTCGGGCCCAGGACTGGTGAAGCCTTCGGAGACCCTGTCCCTCACCTGCACTGTCTCTGGTGGCTCCGTCAGCAGTGGTAGTTACTACTGGAGCTGGATCCGGCAGCCCCCAGGGAAGGGACTGGAGTGGATTGGGTATATCTATTACAGTGGGAGCACCAACTACAACCCCTCCCTCAAGAGTCGAGTCACCATATCAGTAGACACGTCCAAGAACCAGTTCTCCCTGAAGCTGAGCTCTGTGACCGCTGCGGACACGGCCGTGTATTACTGTGCGAGAGAGTATTACTATGATAGTAGTGGTTATTACTACGAATACTT....CCAGCACTGGGGCCAGGGCACCCTGGTCACCGTCTCCTCAG", "", "", "", ""], "indel_reversed_seqs": ["", "CAGGTGCAGCTGCAGGAGTCGGGCCCGGGACTGGTGAAGCCTTCGGAGACCCTGTCCCTCACCTGCACTGTCTCTGGTGGCTCCGTCAGCAGTGGTAGTTACTACTGGAGCTGGATCCGGCAGCCCCCAGGGAAGGGACTGGAGTGGATTGGGTATATCTATTACAGTGGGAGCACCAACTACAACCCCTCCCTCAAGAGTCGAGTCACCATATCAGTAGACACGTCCAAAAACCAGTTCTCGCTGAAGCTGAGCTCTGTGACCGCTGCGGACACGGCCGTGTATTACTGTGCGAGAGAGTATTACTATGATAGTAGTGGTTATTACTACGAATACTTCCAGCATTGGGGCCAGGGCACCCTGGTCACCGTCTCCTCAG", "", "CAGGTGCAGCTGCAGGAGTCGGGTCCAGGACTGATGAAGCCTTCGGAGACCCTGTCCCTCACCTGCACTGTCTCTGGTGGCTCCGTCAGCAGTGGTAGTTACTACTGGAGCTGGATCCGGCAGCCCCCAGCGAAGGGACTGGAGTGGATTGGGTATATCTATTACAGTGGGAGCGCCAACTACAACCCCTCCCTCAAGAGTCGAGTCACCATATCAGTAGACACGTCCAAGAACCAGTTCTCCCTGGAGCTGAGCTCTGTGACCGCTGCGGACACGGCCGTGTATTACTGTGCGAGAAAGTATTACTATGATAGTAGTGGTTATTACTACGAATACTTCCAGCACTGGGGCCAGGGCACCCTGGCCACCGTCTCCTCAG", "", "", "", ""], "reco_id": "e19f613502", "tree": "[&R] (((c7a8a5b2f0:0.011473947230957373,(d9172b4f22:0.011204353580934877,((64de54c978:0.007472444634623492,(b2982a29ea:0.0026644178012223156,21f0e10a44:0.0026644178012223156)lpv:0.004808026833401175)nvx:0.0024335773692030545,(eeca70ed28:0.0016674331281391287,579bc5aa80:0.0016674331281391287)dop:0.008238588875687418)jvx:0.0012983315721083314)inp:0.0002695936561224946)dln:0.0004813332009401619,27eccd7baf:0.011955280430997533)hop:0.0013902674171160023)lmw:0.0;\n", "unique_ids": ["eeca70ed28", "c7a8a5b2f0", "b2982a29ea", "d9172b4f22", "27eccd7baf", "21f0e10a44", "64de54c978", "579bc5aa80"], "invalid": false, "v_gene": "IGHV4-61*01", "d_gene": "IGHD3-22*01", "j_gene": "IGHJ1*01", "cdr3_length": 60, "mut_freqs": [0.013192612137203167, 0.010554089709762533, 0.018469656992084433, 0.018469656992084433, 0.010554089709762533, 0.021108179419525065, 0.005277044854881266, 0.018469656992084433], "n_mutations": [5, 4, 7, 7, 4, 8, 2, 7], "input_seqs": ["CAGGTGCAGCTGCAGGAGTCGGGCCCAGGACTGGTGAAGCCTTCGCAGACCCTGTCCCTCACCTGCACTGTCTCTGGTGGCTCCGTCAGCAGTGGTAGTTACTACTGGAGCTGGATCCGGCAGCCCCCAGGGAAGGGACTGGAGTGGATTGGGTATATCTATTACAGTGGGAGCACCAACTACAACCCCTCCCTCAAGAGTCGAGTCACCATTTCAGTAGACACGTCCAAGAACCAGTTCTCCCTGAAGCTGAGCTCTGTGACCGCTGCGGACACGGGCGTGTATTACTGTGCGAGAGAGTATTACTATGATAGTAGTGGTTATTACTACGGATACTTCCAGCACTGGGGCCAGGGCACCCTGGCCACCGTCTCCTCAG", "CAGGTGCAGCTGCAGGAGTCGGGCCCGGGACTGGTGAAGCCTTCGGAGACCCTGTCTGCACTGTCTCTGGTGGCTCCGTCAGCAGTGGTAGTTACTACTGGAGCTGGATCCGGCAGCCCCCAGGGAAGGGACTGGAGTGGATTGGGTATATCTATTACAGTGGGAGCACCAACTACAACCCCTCCCTCAAGAGTCGAGTCACCATATCAGTAGACACGTCCAAAAACCAGTTCTCGCTGAAGCTGAGCTCTGTGACCGCTGCGGACACGGCCGTGTATTACTGTGCGAGAGAGTATTACTATGAGTGGTTATTACTACGAATACTTCCAGCATTGGGGCCAGGGCACCCTGGTCACCGTCTCCTCAG", "CAGGTGCAACTGCAGGAGTCGGGCCCAGGACTGGTGAAGCCTTCGGAGACCCTGTCCCTCACCTGCACTGTCTCTGGTGGCTCCGTCAGCAGTGGTAGTTACTACTGGAGCTGGATCCGGCAGCCCTCAGGGAAGGGACTGGAGTGGATTGCGTATATCTATTACAGTGGGAGCACTAACTACAACCCCTCCCTGAAGAGTCGAGTCACCATATCAGTAGACACGTCCAAGAACCAGTTCTCCCTGAAGCTGAGCTCTGTGACCGCTGCGGACACGGCCGTGTATTACTGTGCGAGAGGGTATTACTATGATAGTAGTGGTTATTACTACGAATACTTCCAGCACTGGGGCCAGGGCACCCTGGCCACCGTCTCCTCAG", "CAGGTGCAGCTGCAGGAGTCGGGTCCAGGACTGATGAAGCCTTCGGAGACCCTGTCCCTCACCTGCACTGTCTCTGGTGGCTCCGTCAGCAGTGGTAGTTACTACTGGAGCTGGATCCGGCAGCCCCCAGCGAAGGGACTGGAGTGGATTGGGTATATCTATTACAGTGGGAGCGCCAACTACAACCCCTCCCTCAAGAGTCGAGTCACCATATCAGTAGACACGTCCAAGAACCAGCTGAGCTCTGTGACCGCTGCGGACACGGCCGTGTATTACTGTGCGAGAAAGTATTACTATGATAGTAGTGGTTATTACTACGAATACTTCATTCCAGCACTGGGGCCAGGGCACCCTGGCCACCGTCTCCTCAG", "CAGGTGCAGCTGCAGGAGTCGGGCCCAGGACTGGTGAAGCCTTCGGAGACCCTGTCCCTCACCTGCACTATCTCTGGTGGCTCCGTCAGCAGTGGTAGTTACTACTGGAGCTGGATCCGGCAGCCCCCAGGGAAGGGACTGGAGTGGATTGGGTATATCTATCACAGTGGGAGCACCAACTACAACCCCTCCCTCAAGAGTCGAGTCACCATATCAGTAGACACGTTCAAGAACCAGTTCTCCCTGAAGCTGAGCTCTGTGACCGCTGCGGACACGGCCGTGTATTACTGTGCGAGAGAGTATTACTATGATAGTAGTGGTTATTACTACGAATACTTCCAGTACTGGGGCCAGGGCACCCTGGTCACCGTCTCCTCAG", "CAGGTGCAGCTGCAGGAATCGGGCCCAGGACTGGTGAAGCCTTCGGAGACCCTGTCCCTCACCTGCACTGTCTCTGGTGGCTCCGTCAGCAGTGGTAGTTACTACTGGAGCTGGATCCGGCAGCCCTCAGGGAAGGGACTGGAGTGGATTGGGTATATCTATTACAGTGGGAGCACTAACTACCACCCCTCCCTGAAGAGTCGAGTCACCATATCAGTAGACACGTCCAAGAACCAGTTCTCCCTGAAGCTGAGCTCTGTGACCGCTGCGGACACGGCCGTGTATTACTGTGCGAGAGGGTATTACTATGATAGTAGTGGTTATTACTACGAATACTTCCAGCACTGGGGCCAGGGCACCCTGCCCACCGTCTCCTCAG", "CAGGTGCAGCTGCAGGAGTCGGGCCCAGGACTGGTGAAGCCTTCGGAGACCCTGTCCCTCACCTGCACTGTCTCTGGTGGCTCCGTCAGCAGTGGTAGTTACTACTGGAGCTGGATCCGGCAGCCCCCAGGGAAGGGACTGGAGTGGATTGGGTATATCTATTACAGTGGGAGCACCAACTACAACCCCTCCCTCAAGAGTCGAGTCACCATATCAGTAGACACGTCCAAGAACCAGTTCTCCCTGAAGCTGAGCTCTGTGACCGCTGCGGACACGGCCGTGTATTACTGTGCGAGAGGGTATTACTATGATAGTAGTGGTTATTACTACGAATACTTCCAGCACTGGGGCCAGGGCACCCTGGCCACCGTCTCCTCAG", "CAGGTGCAGCTGCAGGAGTTGGGCCCAGGACTGGTGAAGCCTTCGCAGACCCTGTCCCTCACCTGCACTGTCTCTGGTGGCTCCGTCAGCAGTGTTAGTTACTACTGGAGCTGGATCCGGCAGCCCCCAGGGAAGGGACTGGAGTGGATTGGGTATATCTATTACAGTGGGAGCACCAACTACAACCCCTCCCTCAAGAGTCGAGTCACCATTTCAGTAGACACGTCCAAGAACCAGTTCTCCCTGAAGCTGAGCTCTGTGACCGCTGCGGACACGGGCGTGTATTACTGTGCGAGAGAGTATTACTATGATAGTAGTGGTTATTACTACGGATACTTCCAGCACTGGGGCCAGGGCACCCTGGCCACCGTCTCCTCAG"], "has_shm_indels": [false, true, false, true, false, false, false, false], "naive_seq": "CAGGTGCAGCTGCAGGAGTCGGGCCCAGGACTGGTGAAGCCTTCGGAGACCCTGTCCCTCACCTGCACTGTCTCTGGTGGCTCCGTCAGCAGTGGTAGTTACTACTGGAGCTGGATCCGGCAGCCCCCAGGGAAGGGACTGGAGTGGATTGGGTATATCTATTACAGTGGGAGCACCAACTACAACCCCTCCCTCAAGAGTCGAGTCACCATATCAGTAGACACGTCCAAGAACCAGTTCTCCCTGAAGCTGAGCTCTGTGACCGCTGCGGACACGGCCGTGTATTACTGTGCGAGAGAGTATTACTATGATAGTAGTGGTTATTACTACGAATACTTCCAGCACTGGGGCCAGGGCACCCTGGTCACCGTCTCCTCAG", "duplicates": [[], [], [], [], [], [], [], []], "v_3p_del": 0, "d_5p_del": 0, "d_3p_del": 0, "j_5p_del": 3, "v_5p_del": 0, "j_3p_del": 0, "vd_insertion": "", "dj_insertion": "", "fv_insertion": "", "jf_insertion": "", "mutated_invariants": [false, false, false, true, false, false, false, false], "in_frames": [true, false, true, true, true, true, true, true], "stops": [false, true, false, false, false, false, false, false], "loci": ["igh", "igh", "igh", "igh", "igh", "igh", "igh", "igh"], "codon_positions": {"v": 288, "j": 345}}, {"qr_gap_seqs": ["", ""], "gl_gap_seqs": ["", ""], "indel_reversed_seqs": ["", ""], "reco_id": "a7dd2ff3bf", "tree": "[&R] ((f29bce4695:0.0007728403427523895,36d80d25ae:0.0007728403427523895)bin:0.012572707507598646)glt:0.0;\n", "unique_ids": ["f29bce4695", "36d80d25ae"], "invalid": false, "v_gene": "IGHV3-66*02", "d_gene": "IGHD1-20*01", "j_gene": "IGHJ4*02", "cdr3_length": 39, "mut_freqs": [0.008522727272727272, 0.008522727272727272], "n_mutations": [3, 3], "input_seqs": ["GAGGTGCAGCTGGTGGAGTCTGGGGGAGGCTTGGTCCAGCCTGGGGGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCGTCAGTAGCAACTACATGAGCTGGGTCCGCCAGGCTCCAGGGAAGGGGCTGGAGTGGGTCTCAGTTATTTATAGCGGTGGTAGCACATACTACGCAGACTCCGTGAAGAGCCGATTCACCATCTCTAGAGACAATTCCAAGGACACGCTGTATCTTCAAATGAACAGCCTGAGAGCTGAGGACACGGCTGTGTATTACTGTGCGAGAAGTATGATAACTGGTCTCAGAGACTACTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG", "GAGGTGCAGCTGGTGGAGTCTGGGGGAGGCTTGGTCCAGCCTGGGGGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCGTCAGTAGCAACTACATGAGCTGGGTCCGCCAGGCTCCAGGGAAGGGGCTGGAGTGGGTCTCAGTTATTTATAGCGGTGGTAGCACATACTACGCAGACTCCGTGAAGAGCCGATTCACCATCTCTAGAGACAATTCCAAGGACACGCTGTATCTTCAAATGAACAGCCTGAGAGCTGAGGACACGGCTGTGTATTACTGTGCGAGAAGTATGATAACTGGTCTCAGAGACTACTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG"], "has_shm_indels": [false, false], "naive_seq": "GAGGTGCAGCTGGTGGAGTCTGGGGGAGGCTTGGTCCAGCCTGGGGGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCGTCAGTAGCAACTACATGAGCTGGGTCCGCCAGGCTCCAGGGAAGGGGCTGGAGTGGGTCTCAGTTATTTATAGCGGTGGTAGCACATACTACGCAGACTCCGTGAAGGGCCGATTCACCATCTCCAGAGACAATTCCAAGAACACGCTGTATCTTCAAATGAACAGCCTGAGAGCTGAGGACACGGCTGTGTATTACTGTGCGAGAAGTATGATAACTGGTCTCAGAGACTACTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG", "duplicates": [[], []], "v_3p_del": 2, "d_5p_del": 3, "d_3p_del": 7, "j_5p_del": 8, "v_5p_del": 0, "j_3p_del": 0, "vd_insertion": "AGTATG", "dj_insertion": "GTCTCAGA", "fv_insertion": "", "jf_insertion": "", "mutated_invariants": [false, false], "in_frames": [true, true], "stops": [false, false], "loci": ["igh", "igh"], "codon_positions": {"v": 282, "j": 318}}, {"qr_gap_seqs": ["", ""], "gl_gap_seqs": ["", ""], "indel_reversed_seqs": ["", ""], "reco_id": "962999a75d", "tree": "[&R] ((d024e5cab0:-0.0,822801f8ab:-0.0)dkw:-0.0)agk:0.0;\n", "unique_ids": ["d024e5cab0", "822801f8ab"], "invalid": false, "v_gene": "IGHV3-66*02", "d_gene": "IGHD6-13*01", "j_gene": "IGHJ4*02", "cdr3_length": 33, "mut_freqs": [0.0, 0.0], "n_mutations": [0, 0], "input_seqs": ["GAGGTGCAGCTGGTGGAGTCTGGGGGAGGCTTGGTCCAGCCTGGGGGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCGTCAGTAGCAACTACATGAGCTGGGTCCGCCAGGCTCCAGGGAAGGGGCTGGAGTGGGTCTCAGTTATTTATAGCGGTGGTAGCACATACTACGCAGACTCCGTGAAGGGCCGATTCACCATCTCCAGAGACAATTCCAAGAACACGCTGTATCTTCAAATGAACAGCCTGAGAGCTGAGGACACGGCTGTGTATTACTGTGCGAGATCTATAGCAGCAGCCGACTACTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG", "GAGGTGCAGCTGGTGGAGTCTGGGGGAGGCTTGGTCCAGCCTGGGGGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCGTCAGTAGCAACTACATGAGCTGGGTCCGCCAGGCTCCAGGGAAGGGGCTGGAGTGGGTCTCAGTTATTTATAGCGGTGGTAGCACATACTACGCAGACTCCGTGAAGGGCCGATTCACCATCTCCAGAGACAATTCCAAGAACACGCTGTATCTTCAAATGAACAGCCTGAGAGCTGAGGACACGGCTGTGTATTACTGTGCGAGATCTATAGCAGCAGCCGACTACTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG"], "has_shm_indels": [false, false], "naive_seq": "GAGGTGCAGCTGGTGGAGTCTGGGGGAGGCTTGGTCCAGCCTGGGGGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCGTCAGTAGCAACTACATGAGCTGGGTCCGCCAGGCTCCAGGGAAGGGGCTGGAGTGGGTCTCAGTTATTTATAGCGGTGGTAGCACATACTACGCAGACTCCGTGAAGGGCCGATTCACCATCTCCAGAGACAATTCCAAGAACACGCTGTATCTTCAAATGAACAGCCTGAGAGCTGAGGACACGGCTGTGTATTACTGTGCGAGATCTATAGCAGCAGCCGACTACTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG", "duplicates": [[], []], "v_3p_del": 2, "d_5p_del": 3, "d_3p_del": 6, "j_5p_del": 8, "v_5p_del": 0, "j_3p_del": 0, "vd_insertion": "TC", "dj_insertion": "C", "fv_insertion": "", "jf_insertion": "", "mutated_invariants": [false, false], "in_frames": [true, true], "stops": [false, false], "loci": ["igh", "igh"], "codon_positions": {"v": 282, "j": 312}}, {"qr_gap_seqs": [""], "gl_gap_seqs": [""], "indel_reversed_seqs": [""], "reco_id": "91f77d882f", "tree": "[&R] (c19efdaf0d:0.018750976654062952)ios:0.0;\n", "unique_ids": ["c19efdaf0d"], "invalid": false, "v_gene": "IGHV5-51*01", "d_gene": "IGHD6-19*01", "j_gene": "IGHJ4*02", "cdr3_length": 48, "mut_freqs": [0.019230769230769232], "n_mutations": [7], "input_seqs": ["GAGGTGCAGCTTGTGCAGTCTGGAGCAGAGGTGAAAAAGCCCGGGGAGTCTCTGAAGATCTCCTGTAAGGGTTCTGGATACAGCTTTACCAGCTATTGGATCGGCTGGGTGCGCCAGATGCCCGGGAAAGGCCTGGACTGGATGGGGATCATCTATCCTGGTGACTCTGATACCAGATACAGCCCGTCCTTCCAAGGCCATGTCACCATCTCAGCCGACAAGTCCATCAGCACCGCCTACCTGGCGTGGAGCAGCCTGAAGGCCTCGGACACCGCCATGTATTACTGTGCGAGACTAGGGTATAGCAGTGGCTGGTAGTCGTTTGACTACTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG"], "has_shm_indels": [false], "naive_seq": "GAGGTGCAGCTGGTGCAGTCTGGAGCAGAGGTGAAAAAGCCCGGGGAGTCTCTGAAGATCTCCTGTAAGGGTTCTGGATACAGCTTTACCAGCTACTGGATCGGCTGGGTGCGCCAGATGCCCGGGAAAGGCCTGGAGTGGATGGGGATCATCTATCCTGGTGACTCTGATACCAGATACAGCCCGTCCTTCCAAGGCCAGGTCACCATCTCAGCCGACAAGTCCATCAGCACCGCCTACCTGCAGTGGAGCAGCCTGAAGGCCTCGGACACCGCCATGTATTACTGTGCGAGACTAGGGTATAGCAGTGGCTGGTACTCGTTTGACTACTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG", "duplicates": [[]], "v_3p_del": 1, "d_5p_del": 0, "d_3p_del": 0, "j_5p_del": 5, "v_5p_del": 0, "j_3p_del": 0, "vd_insertion": "TA", "dj_insertion": "TCG", "fv_insertion": "", "jf_insertion": "", "mutated_invariants": [false], "in_frames": [true], "stops": [true], "loci": ["igh"], "codon_positions": {"v": 285, "j": 330}}, {"qr_gap_seqs": [""], "gl_gap_seqs": [""], "indel_reversed_seqs": [""], "reco_id": "256bc9b5ab", "tree": "[&R] (5f7b69c48f:0.018750976654062952)efl:0.0;\n", "unique_ids": ["5f7b69c48f"], "invalid": false, "v_gene": "IGHV3-66*02", "d_gene": "IGHD6-6*01", "j_gene": "IGHJ4*02", "cdr3_length": 57, "mut_freqs": [0.016216216216216217], "n_mutations": [6], "input_seqs": ["GAGGTGCAGCTGGTGTAGTCTGGGGGAGGCTTGGTCCAGCCTGGGGCGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCATTAGTAGCAACTACATGAGCTGGGTCCGCCAGGCTCCAGGGAAGGGGCTGGAGTGGGTCTCAGTTATTTATAGCGGTGGTAGCACATACTACGCAGACTCCGTGAAGGGCCGATTCAGCATCTCCAGAGACAATTCCAAGAACACGCTGTATCTTCAAATGAACAGCCTGAGACCTGAGGACACGGCTGTGTATTACTGTGCGAGAGAGTTTTGTGTCGGCAGGAGTATAGCAGCAGGGCGCCCTGACTACTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG"], "has_shm_indels": [false], "naive_seq": "GAGGTGCAGCTGGTGGAGTCTGGGGGAGGCTTGGTCCAGCCTGGGGGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCGTCAGTAGCAACTACATGAGCTGGGTCCGCCAGGCTCCAGGGAAGGGGCTGGAGTGGGTCTCAGTTATTTATAGCGGTGGTAGCACATACTACGCAGACTCCGTGAAGGGCCGATTCACCATCTCCAGAGACAATTCCAAGAACACGCTGTATCTTCAAATGAACAGCCTGAGAGCTGAGGACACGGCTGTGTATTACTGTGCGAGAGAGTTTTGTGTCGGCAGGAGTATAGCAGCAGGGCGCCCTGACTACTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG", "duplicates": [[]], "v_3p_del": 0, "d_5p_del": 0, "d_3p_del": 6, "j_5p_del": 7, "v_5p_del": 0, "j_3p_del": 0, "vd_insertion": "GTTTTGTGTCGGCAG", "dj_insertion": "AGGGCGCCC", "fv_insertion": "", "jf_insertion": "", "mutated_invariants": [false], "in_frames": [true], "stops": [true], "loci": ["igh"], "codon_positions": {"v": 282, "j": 336}}]}
1
+ {"version-info": {"partis-yaml": 0.1, "partis-git": ""}, "germline-info": {"locus": "igh", "functionalities": {}, "seqs": {"v": {"IGHV1-18*01": "CAGGTTCAGCTGGTGCAGTCTGGAGCTGAGGTGAAGAAGCCTGGGGCCTCAGTGAAGGTCTCCTGCAAGGCTTCTGGTTACACCTTTACCAGCTATGGTATCAGCTGGGTGCGACAGGCCCCTGGACAAGGGCTTGAGTGGATGGGATGGATCAGCGCTTACAATGGTAACACAAACTATGCACAGAAGCTCCAGGGCAGAGTCACCATGACCACAGACACATCCACGAGCACAGCCTACATGGAGCTGAGGAGCCTGAGATCTGACGACACGGCCGTGTATTACTGTGCGAGAGA", "IGHV1-2*02": "CAGGTGCAGCTGGTGCAGTCTGGGGCTGAGGTGAAGAAGCCTGGGGCCTCAGTGAAGGTCTCCTGCAAGGCTTCTGGATACACCTTCACCGGCTACTATATGCACTGGGTGCGACAGGCCCCTGGACAAGGGCTTGAGTGGATGGGATGGATCAACCCTAACAGTGGTGGCACAAACTATGCACAGAAGTTTCAGGGCAGGGTCACCATGACCAGGGACACGTCCATCAGCACAGCCTACATGGAGCTGAGCAGGCTGAGATCTGACGACACGGCCGTGTATTACTGTGCGAGAGA", "IGHV2-5*02": "CAGATCACCTTGAAGGAGTCTGGTCCTACGCTGGTGAAACCCACACAGACCCTCACGCTGACCTGCACCTTCTCTGGGTTCTCACTCAGCACTAGTGGAGTGGGTGTGGGCTGGATCCGTCAGCCCCCAGGAAAGGCCCTGGAGTGGCTTGCACTCATTTATTGGGATGATGATAAGCGCTACAGCCCATCTCTGAAGAGCAGGCTCACCATCACCAAGGACACCTCCAAAAACCAGGTGGTCCTTACAATGACCAACATGGACCCTGTGGACACAGCCACATATTACTGTGCACACAGAC", "IGHV2-70D*04": "CAGGTCACCTTGAAGGAGTCTGGTCCTGCGCTGGTGAAACCCACACAGACCCTCACACTGACCTGCACCTTCTCTGGGTTCTCACTCAGCACTAGTGGAATGCGTGTGAGCTGGATCCGTCAGCCCCCAGGGAAGGCCCTGGAGTGGCTTGCACGCATTGATTGGGATGATGATAAATTCTACAGCACATCTCTGAAGACCAGGCTCACCATCTCCAAGGACACCTCCAAAAACCAGGTGGTCCTTACAATGACCAACATGGACCCTGTGGACACAGCCACGTATTACTGTGCACGGATAC", "IGHV3-11*04": "CAGGTGCAGCTGGTGGAGTCTGGGGGAGGCTTGGTCAAGCCTGGAGGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCTTCAGTGACTACTACATGAGCTGGATCCGCCAGGCTCCAGGGAAGGGGCTGGAGTGGGTTTCATACATTAGTAGTAGTGGTAGTACCATATACTACGCAGACTCTGTGAAGGGCCGATTCACCATCTCCAGGGACAACGCCAAGAACTCACTGTATCTGCAAATGAACAGCCTGAGAGCCGAGGACACGGCTGTGTATTACTGTGCGAGAGA", "IGHV3-23*01": "GAGGTGCAGCTGTTGGAGTCTGGGGGAGGCTTGGTACAGCCTGGGGGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCTTTAGCAGCTATGCCATGAGCTGGGTCCGCCAGGCTCCAGGGAAGGGGCTGGAGTGGGTCTCAGCTATTAGTGGTAGTGGTGGTAGCACATACTACGCAGACTCCGTGAAGGGCCGGTTCACCATCTCCAGAGACAATTCCAAGAACACGCTGTATCTGCAAATGAACAGCCTGAGAGCCGAGGACACGGCCGTATATTACTGTGCGAAAGA", "IGHV3-66*02": "GAGGTGCAGCTGGTGGAGTCTGGGGGAGGCTTGGTCCAGCCTGGGGGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCGTCAGTAGCAACTACATGAGCTGGGTCCGCCAGGCTCCAGGGAAGGGGCTGGAGTGGGTCTCAGTTATTTATAGCGGTGGTAGCACATACTACGCAGACTCCGTGAAGGGCCGATTCACCATCTCCAGAGACAATTCCAAGAACACGCTGTATCTTCAAATGAACAGCCTGAGAGCTGAGGACACGGCTGTGTATTACTGTGCGAGAGA", "IGHV3-69-1*02": "GAGGTGCAGCTGGTGGAGTCTGGGGGAGGCTTGGTAAAGCCTGGGGGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCTTCAGTGACTACTACATGAACTGGGTCCGCCAGGCTCCAGGGAAGGGGCTGGAGTGGGTCTCATCCATTAGTAGTAGTAGTACCATATACTACGCAGACTCTGTGAAGGGCCGATTCACCATCTCCAGAGACAACGCCAAGAACTCACTGTATCTGCAAATGAACAGCCTGAGAGCCGAGGACACGGCTGTTTATTACTGTGCGAGAGA", "IGHV3-7*05": "GAGGTGCAGCTGGTGGAGTCTGGGGGAGGCTTGGTCCAGCCTGGGGGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCTTTAGTAGCTATTGGATGAGCTGGGTCCGCCAGGCTCCAGGGAAAGGGCTGGAGTGGGTGGCCAACATAAAGCAAGATGGAAGTGAGAAATACTATGTGGACTCTGTGAAGGGCCGATTCACCATCTCCAGAGACAACGCCAAGAACTCACTGTATCTGCAAATGAACAGCCTGAGAGCCGAGGACACGGCCGTGTATTACTGTGCGAGAGA", "IGHV3-9*02": "GAAGTGCAGCTGGTGGAGTCTGGGGGAGGCTTGGTACAGCCTGGCAGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCTCTGATGATTATGCCATGCACTGGGTCCGGCAAGCTCCAGGGAAGGGCCTGGAGTGGGTCTCAGGTATTAGTTGGAATAGTGGTAGCATAGGCTATGCGGACTCTGTGAAGGGCCGATTCACCATCTCCAGAGACAACGCCAAGAACTCCCTGTATCTGCAAATGAACAGTCTGAGAGCTGAGGACACGGCCTTGTATTACTGTGCAAAAGATA", "IGHV4-34*01": "CAGGTGCAGCTACAGCAGTGGGGCGCAGGACTGTTGAAGCCTTCGGAGACCCTGTCCCTCACCTGCGCTGTCTATGGTGGGTCCTTCAGTGGTTACTACTGGAGCTGGATCCGCCAGCCCCCAGGGAAGGGGCTGGAGTGGATTGGGGAAATCAATCATAGTGGAAGCACCAACTACAACCCGTCCCTCAAGAGTCGAGTCACCATATCAGTAGACACGTCCAAGAACCAGTTCTCCCTGAAGCTGAGCTCTGTGACCGCCGCGGACACGGCTGTGTATTACTGTGCGAGAGG", "IGHV4-39*09": "CAGCTGCAGCTGCAGGAGTCGGGCCCAGGACTGGTGAAGCCTTCGGAGACCCTGTCCCTCACCTGCACTGTCTCTGGTGGCTCCATCAGCAGTAGTAGTTACTACTGGGGCTGGATCCGCCAGCCCCCAGGGAAGGGGCTGGAGTGGATTGGGAGTATCTATTATAGTGGGAGCACCTACTACAACCCGTCCCTCAAGAGTCGAGTCACCATATCAGTAGACACGTCCAAGAACCAGTTCTCCCTGAAGCTGAGCTCTGTGACCGCAGCGGACACGGCCGTGTATTACTGTGCGAGAGA", "IGHV4-4*09": "CAGGTGCAGCTGCAGGAGTCGGGCCCAGGACTGGTGAAGCCTTCGGAGACCCTGTCCCTCACCTGCACTGTCTCTGGTGGCTCCATCAGTAGTTACTACTGGAGCTGGATCCGGCAGCCCCCAGGGAAGGGACTGGAGTGGATTGGGTACATCTATACCAGTGGGAGCACCAACTACAACCCCTCCCTCAAGAGTCGAGTCACCATATCAGTAGACACGTCCAAGAACCAGTTCTCCCTGAAGCTGAGCTCTGTGACCGCCGCAGACACGGCCGTGTATTACTGTGCGAGAGA", "IGHV4-61*01": "CAGGTGCAGCTGCAGGAGTCGGGCCCAGGACTGGTGAAGCCTTCGGAGACCCTGTCCCTCACCTGCACTGTCTCTGGTGGCTCCGTCAGCAGTGGTAGTTACTACTGGAGCTGGATCCGGCAGCCCCCAGGGAAGGGACTGGAGTGGATTGGGTATATCTATTACAGTGGGAGCACCAACTACAACCCCTCCCTCAAGAGTCGAGTCACCATATCAGTAGACACGTCCAAGAACCAGTTCTCCCTGAAGCTGAGCTCTGTGACCGCTGCGGACACGGCCGTGTATTACTGTGCGAGAGA", "IGHV5-51*01": "GAGGTGCAGCTGGTGCAGTCTGGAGCAGAGGTGAAAAAGCCCGGGGAGTCTCTGAAGATCTCCTGTAAGGGTTCTGGATACAGCTTTACCAGCTACTGGATCGGCTGGGTGCGCCAGATGCCCGGGAAAGGCCTGGAGTGGATGGGGATCATCTATCCTGGTGACTCTGATACCAGATACAGCCCGTCCTTCCAAGGCCAGGTCACCATCTCAGCCGACAAGTCCATCAGCACCGCCTACCTGCAGTGGAGCAGCCTGAAGGCCTCGGACACCGCCATGTATTACTGTGCGAGACA"}, "d": {"IGHD1-20*01": "GGTATAACTGGAACGAC", "IGHD1-26*01": "GGTATAGTGGGAGCTACTAC", "IGHD2-15*01": "AGGATATTGTAGTGGTGGTAGCTGCTACTCC", "IGHD2-2*01": "AGGATATTGTAGTAGTACCAGCTGCTATGCC", "IGHD2-21*01": "AGCATATTGTGGTGGTGATTGCTATTCC", "IGHD2-21*02": "AGCATATTGTGGTGGTGACTGCTATTCC", "IGHD2-8*01": "AGGATATTGTACTAATGGTGTATGCTATACC", "IGHD2-8*02": "AGGATATTGTACTGGTGGTGTATGCTATACC", "IGHD3-10*01": "GTATTACTATGGTTCGGGGAGTTATTATAAC", "IGHD3-10*03": "GTATTACTATGGTTCAGGGAGTTATTATAAC", "IGHD3-16*02": "GTATTATGATTACGTTTGGGGGAGTTATCGTTATACC", "IGHD3-22*01": "GTATTACTATGATAGTAGTGGTTATTACTAC", "IGHD3-3*01": "GTATTACGATTTTTGGAGTGGTTATTATACC", "IGHD4-17*01": "TGACTACGGTGACTAC", "IGHD4-4*01": "TGACTACAGTAACTAC", "IGHD5-5*01": "GTGGATACAGCTATGGTTAC", "IGHD6-13*01": "GGGTATAGCAGCAGCTGGTAC", "IGHD6-19*01": "GGGTATAGCAGTGGCTGGTAC", "IGHD6-6*01": "GAGTATAGCAGCTCGTCC"}, "j": {"IGHJ1*01": "GCTGAATACTTCCAGCACTGGGGCCAGGGCACCCTGGTCACCGTCTCCTCAG", "IGHJ2*01": "CTACTGGTACTTCGATCTCTGGGGCCGTGGCACCCTGGTCACTGTCTCCTCAG", "IGHJ3*02": "TGATGCTTTTGATATCTGGGGCCAAGGGACAATGGTCACCGTCTCTTCAG", "IGHJ4*02": "ACTACTTTGACTACTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG", "IGHJ5*02": "ACAACTGGTTCGACCCCTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG", "IGHJ6*02": "ATTACTACTACTACTACGGTATGGACGTCTGGGGCCAAGGGACCACGGTCACCGTCTCCTCAG", "IGHJ6*03": "ATTACTACTACTACTACTACATGGACGTCTGGGGCAAAGGGACCACGGTCACCGTCTCCTCAG"}}, "cyst-positions": {"IGHV2-5*02": 288, "IGHV4-34*01": 282, "IGHV1-2*02": 285, "IGHV1-18*01": 285, "IGHV3-7*05": 285, "IGHV3-69-1*02": 282, "IGHV3-11*04": 285, "IGHV2-70D*04": 288, "IGHV5-51*01": 285, "IGHV3-66*02": 282, "IGHV4-39*09": 288, "IGHV3-9*02": 285, "IGHV3-23*01": 285, "IGHV4-61*01": 288, "IGHV4-4*09": 282}, "tryp-positions": {"IGHJ4*02": 14, "IGHJ2*01": 19, "IGHJ3*02": 16, "IGHJ6*02": 29, "IGHJ5*02": 17, "IGHJ1*01": 18, "IGHJ6*03": 29}}, "partitions": [{"logprob": 0.0, "n_clusters": 10, "n_procs": 1, "partition": [["853dd8e975", "f05be2a44f", "311949d4db", "3e69b1acce", "e0b1f6f1e6", "bba6cb99ec"], ["aae1c603d3", "7ebc1b7976", "94983a83cd", "8f2172ddde", "9114fc4533"], ["3d5e18cedd", "a834c46736"], ["5f4c456471", "651dbac867", "22ffeb5acc", "3f6a0e8f92", "35820aac9c", "cf0720f18a", "83a311c688", "c922857e00", "e783280f21", "fed0b82e9c", "7c7e2d39ac"], ["a32918fa7c", "d76f52b01a", "0b027c31ea", "3cd1599613"], ["49516f50c8", "775dc4cd18", "f6a0022f12", "437bff5b48", "a366840534", "6be16277dd", "64ae95318c", "e45374ef7b", "5ad57efbb9", "16caab20bd", "aa6e1a8781", "1a680fb189", "bb706a907c", "aa7dae44c3", "dc6a919315", "25edd0ce47", "f1712e10a7", "1fa3a3147c", "340e539235", "79997552ff", "7a63383c3f", "a8a845afd0"], ["e2c05b0558", "fdba07f2d2", "e86b47e3d3", "7e5c759f54", "ae9764988c", "6b13522970", "d4ce68d359", "cd9bc63afe", "ac52a46bb0", "6c21770612", "dd511fd81e", "46e0a1c5ce"], ["24845562e3", "501a887172", "f168b0ec8b"], ["5798aae16b", "01430d7987", "5ac6e92281", "7c463a8e7c", "37921756cc"], ["deaadfc443", "748a35a278", "a646646bdb", "84f52131d2"]]}], "events": [{"qr_gap_seqs": ["", "", "", "", "", "GAGGTGCAGCTGGTGGAGTCTGGGGGAGGCTTGGTCC........GGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCTTTAGTAGCTATTGGATGAGCTGGGTCCGCCAGGCTCCAGGGAAAGGGCTGGAGTGGGTGGCCAACATAAAGCAAGATGGAAGTGAGAAATACTATGTGGACTCTGTGAAGGGCCGATTCACCATCTCCAGAGACAACGCCAAGAACTCACTGTATCTGCAAATGAACAGCCTGAGAGCCGAGGACACGGCCGTGTATTACTGTGCGAGAGACTGCGAAGCAGCTGGTACCTATTCTAAGTTGCGTGAGGGTATGGACGTCTGGGGCCAAGGGACCAC........TCTCCTCAG"], "gl_gap_seqs": ["", "", "", "", "", "GAGGTGCAGCTGGTGGAGTCTGGGGGAGGCTTGGTCCAGCCTGGGGGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCTTTAGTAGCTATTGGATGAGCTGGGTCCGCCAGGCTCCAGGGAAAGGGCTGGAGTGGGTGGCCAACATAAAGCAAGATGGAAGTGAGAAATACTATGTGGACTCTGTGAAGGGCCGATTCACCATCTCCAGAGACAACGCCAAGAACTCACTGTATCTGCAAATGAACAGCCTGAGAGCCGAGGACACGGCCGTGTATTACTGTGCGAGAGACTGCGAAGCAGCTGGTACCTATTCTAAGTTGCGTGAGGGTATGGACGTCTGGGGCCAAGGGACCACGGTCACCGTCTCCTCAG"], "indel_reversed_seqs": ["", "", "", "", "", "GAGGTGCAGCTGGTGGAGTCTGGGGGAGGCTTGGTCCAGCCTGGGGGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCTTTAGTAGCTATTGGATGAGCTGGGTCCGCCAGGCTCCAGGGAAAGGGCTGGAGTGGGTGGCCAACATAAAGCAAGATGGAAGTGAGAAATACTATGTGGACTCTGTGAAGGGCCGATTCACCATCTCCAGAGACAACGCCAAGAACTCACTGTATCTGCAAATGAACAGCCTGAGAGCCGAGGACACGGCCGTGTATTACTGTGCGAGAGACTGCGAAGCAGCTGGTACCTATTCTAAGTTGCGTGAGGGTATGGACGTCTGGGGCCAAGGGACCACGGTCACCGTCTCCTCAG"], "reco_id": "5611db2b0a", "tree": "[&R] (((bba6cb99ec:-0.0,(311949d4db:-0.0,(f05be2a44f:-0.0,(3e69b1acce:-0.0,e0b1f6f1e6:-0.0)hix:-0.0)ehs:-0.0)fmw:-0.0)fhu:-0.0,853dd8e975:-0.0)fty:-0.0)ael:0.0;\n", "unique_ids": ["853dd8e975", "f05be2a44f", "311949d4db", "3e69b1acce", "e0b1f6f1e6", "bba6cb99ec"], "invalid": false, "v_gene": "IGHV3-7*05", "d_gene": "IGHD6-13*01", "j_gene": "IGHJ6*02", "cdr3_length": 63, "mut_freqs": [0.0, 0.0, 0.0, 0.0, 0.0, 0.0], "n_mutations": [0, 0, 0, 0, 0, 0], "input_seqs": ["GAGGTGCAGCTGGTGGAGTCTGGGGGAGGCTTGGTCCAGCCTGGGGGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCTTTAGTAGCTATTGGATGAGCTGGGTCCGCCAGGCTCCAGGGAAAGGGCTGGAGTGGGTGGCCAACATAAAGCAAGATGGAAGTGAGAAATACTATGTGGACTCTGTGAAGGGCCGATTCACCATCTCCAGAGACAACGCCAAGAACTCACTGTATCTGCAAATGAACAGCCTGAGAGCCGAGGACACGGCCGTGTATTACTGTGCGAGAGACTGCGAAGCAGCTGGTACCTATTCTAAGTTGCGTGAGGGTATGGACGTCTGGGGCCAAGGGACCACGGTCACCGTCTCCTCAG", "GAGGTGCAGCTGGTGGAGTCTGGGGGAGGCTTGGTCCAGCCTGGGGGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCTTTAGTAGCTATTGGATGAGCTGGGTCCGCCAGGCTCCAGGGAAAGGGCTGGAGTGGGTGGCCAACATAAAGCAAGATGGAAGTGAGAAATACTATGTGGACTCTGTGAAGGGCCGATTCACCATCTCCAGAGACAACGCCAAGAACTCACTGTATCTGCAAATGAACAGCCTGAGAGCCGAGGACACGGCCGTGTATTACTGTGCGAGAGACTGCGAAGCAGCTGGTACCTATTCTAAGTTGCGTGAGGGTATGGACGTCTGGGGCCAAGGGACCACGGTCACCGTCTCCTCAG", "GAGGTGCAGCTGGTGGAGTCTGGGGGAGGCTTGGTCCAGCCTGGGGGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCTTTAGTAGCTATTGGATGAGCTGGGTCCGCCAGGCTCCAGGGAAAGGGCTGGAGTGGGTGGCCAACATAAAGCAAGATGGAAGTGAGAAATACTATGTGGACTCTGTGAAGGGCCGATTCACCATCTCCAGAGACAACGCCAAGAACTCACTGTATCTGCAAATGAACAGCCTGAGAGCCGAGGACACGGCCGTGTATTACTGTGCGAGAGACTGCGAAGCAGCTGGTACCTATTCTAAGTTGCGTGAGGGTATGGACGTCTGGGGCCAAGGGACCACGGTCACCGTCTCCTCAG", "GAGGTGCAGCTGGTGGAGTCTGGGGGAGGCTTGGTCCAGCCTGGGGGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCTTTAGTAGCTATTGGATGAGCTGGGTCCGCCAGGCTCCAGGGAAAGGGCTGGAGTGGGTGGCCAACATAAAGCAAGATGGAAGTGAGAAATACTATGTGGACTCTGTGAAGGGCCGATTCACCATCTCCAGAGACAACGCCAAGAACTCACTGTATCTGCAAATGAACAGCCTGAGAGCCGAGGACACGGCCGTGTATTACTGTGCGAGAGACTGCGAAGCAGCTGGTACCTATTCTAAGTTGCGTGAGGGTATGGACGTCTGGGGCCAAGGGACCACGGTCACCGTCTCCTCAG", "GAGGTGCAGCTGGTGGAGTCTGGGGGAGGCTTGGTCCAGCCTGGGGGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCTTTAGTAGCTATTGGATGAGCTGGGTCCGCCAGGCTCCAGGGAAAGGGCTGGAGTGGGTGGCCAACATAAAGCAAGATGGAAGTGAGAAATACTATGTGGACTCTGTGAAGGGCCGATTCACCATCTCCAGAGACAACGCCAAGAACTCACTGTATCTGCAAATGAACAGCCTGAGAGCCGAGGACACGGCCGTGTATTACTGTGCGAGAGACTGCGAAGCAGCTGGTACCTATTCTAAGTTGCGTGAGGGTATGGACGTCTGGGGCCAAGGGACCACGGTCACCGTCTCCTCAG", "GAGGTGCAGCTGGTGGAGTCTGGGGGAGGCTTGGTCCGGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCTTTAGTAGCTATTGGATGAGCTGGGTCCGCCAGGCTCCAGGGAAAGGGCTGGAGTGGGTGGCCAACATAAAGCAAGATGGAAGTGAGAAATACTATGTGGACTCTGTGAAGGGCCGATTCACCATCTCCAGAGACAACGCCAAGAACTCACTGTATCTGCAAATGAACAGCCTGAGAGCCGAGGACACGGCCGTGTATTACTGTGCGAGAGACTGCGAAGCAGCTGGTACCTATTCTAAGTTGCGTGAGGGTATGGACGTCTGGGGCCAAGGGACCACTCTCCTCAG"], "has_shm_indels": [false, false, false, false, false, true], "naive_seq": "GAGGTGCAGCTGGTGGAGTCTGGGGGAGGCTTGGTCCAGCCTGGGGGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCTTTAGTAGCTATTGGATGAGCTGGGTCCGCCAGGCTCCAGGGAAAGGGCTGGAGTGGGTGGCCAACATAAAGCAAGATGGAAGTGAGAAATACTATGTGGACTCTGTGAAGGGCCGATTCACCATCTCCAGAGACAACGCCAAGAACTCACTGTATCTGCAAATGAACAGCCTGAGAGCCGAGGACACGGCCGTGTATTACTGTGCGAGAGACTGCGAAGCAGCTGGTACCTATTCTAAGTTGCGTGAGGGTATGGACGTCTGGGGCCAAGGGACCACGGTCACCGTCTCCTCAG", "duplicates": [[], [], [], [], [], []], "v_3p_del": 0, "d_5p_del": 9, "d_3p_del": 0, "j_5p_del": 17, "v_5p_del": 0, "j_3p_del": 0, "vd_insertion": "CTGCGA", "dj_insertion": "CTATTCTAAGTTGCGTGAG", "fv_insertion": "", "jf_insertion": "", "mutated_invariants": [false, false, false, false, false, false], "in_frames": [true, true, true, true, true, false], "stops": [false, false, false, false, false, true], "loci": ["igh", "igh", "igh", "igh", "igh", "igh"], "codon_positions": {"v": 285, "j": 345}}, {"qr_gap_seqs": ["", "", "", "", ""], "gl_gap_seqs": ["", "", "", "", ""], "indel_reversed_seqs": ["", "", "", "", ""], "reco_id": "fbdf4feea6", "tree": "[&R] ((((aae1c603d3:0.000683433671244433,8f2172ddde:0.000683433671244433)lqs:0.004278868810403198,94983a83cd:0.00496230248067712)fhp:0.002822409825460986,(7ebc1b7976:0.00028116304094005133,9114fc4533:0.00028116304094005133)aru:0.007503549267139076)pqz:0.00019408634648909498)ahx:0.0;\n", "unique_ids": ["aae1c603d3", "7ebc1b7976", "94983a83cd", "8f2172ddde", "9114fc4533"], "invalid": false, "v_gene": "IGHV3-66*02", "d_gene": "IGHD6-13*01", "j_gene": "IGHJ4*02", "cdr3_length": 33, "mut_freqs": [0.008670520231213872, 0.02023121387283237, 0.014450867052023121, 0.008670520231213872, 0.02023121387283237], "n_mutations": [3, 7, 5, 3, 7], "input_seqs": ["GAGGTGCAGCTGGTGGAGTCTGGGGGAGGCTTGGTCCAGCCTGGGGGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACTGTCACTAGCAACTACATGAGCTGGGTCCGCCAGGCTCCAGGGAAGGGGCTGGAGTAGGTCTCAGTTATTTATAGCGGTGGTAGCACATACTACGCAGACTCCGTGAAGGGCCGATTCACCATCTCCAGAGACAATTCCAAGAACACGCTGTATCTTCAAATGAACAGCCTGAGAGCTGAGGACACGGCTGTGTATTACTGTGCGAGATCTATAGCAGCAGCCGACTACTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG", "GAGGTGCAGCTGGTGGAGTCTGGGGGAGGCTTGGTCCAGCCTGGGGGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCGTCGGTAGCAACTACATGAGCTAGGTCCGCCAGGCTCCAGGGAAGGGGCTGGAGTAGGTCTCAGTTATTTATAGCGGTGGTAGCACATACTACGCAGACTCCGTGAAGGGCCGATTCACCATCTCCAGGGACAATTCGAAGAGCACGCTGTATCTTCAAATAAACAGCCTGAGAGCTGAGGACACGGCTGTGTATTACTGTGCGAGATCTATAGCAGCAGCCGACTACTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG", "GAGGTGCAGCTGGTGAAGTCTGGGGGAGGCTTGGTCCAGCCTGGGGGGTTCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCGTCAGTAGCAACTACATGAGCTGGGTCCGCCAGGCTCCAGGGAAGGGGCTGGAGTGGGTCTCAGTTATTTATAGCGGTGGTAGCACATACTACGCAGACTCCGTGAAGGGCCGATTCACCATCTCCAGAGACACTTCCAAGAACACGCTGTATCTTCAAATGAACAGCCTGAGAGCTCAGGACACGGCTGTGTATTACTGTGCGAGATCCATAGCAGCAGCCGACTACTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG", "GGGGTGCAGCTGGTGGAGTCTGGGGGAGGCTTGGTCCAGCCTGGGGGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCGTCACTAGCAACTACATGAGCTGGGTCCGCCAGGCTCCAGGGAAGGGGCTGGAGTAGGTCTCAGTTATTTATAGCGGTGGTAGCACATACTACGCAGACTCCGTGAAGGGCCGATTCACCATCTCCAGAGACAATTCCAAGAACACGCTGTATCTTCAAATGAACAGCCTGAGAGCTGAGGACACGGCTGTGTATTACTGTGCGAGATCTATAGCAGCAGCCGACTACTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG", "GAGGTGCAGCTGGTGGAGTCTGGGGGAGGCTTGGTCCAGCCTGGGGGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCGTCGGTAGCAACTACATGAGCTAGGTCCGCCAGGCTCCAGGGAAGGGGCTGGAGTAGGTCTCAGTTATTTATAGCGGTGGTAGCACATACTACGCAGACTCCGTGAAGGGCCGATTCACCATCTCCAGGGACAATTCGAAGAGCACGCTGTATCTTCAAATAAACAGCCTGAGAGCTGAGGACACGGCTGTGTATTACTGTGCGAGATCTATAGCAGCAGCCGACTACTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG"], "has_shm_indels": [false, false, false, false, false], "naive_seq": "GAGGTGCAGCTGGTGGAGTCTGGGGGAGGCTTGGTCCAGCCTGGGGGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCGTCAGTAGCAACTACATGAGCTGGGTCCGCCAGGCTCCAGGGAAGGGGCTGGAGTGGGTCTCAGTTATTTATAGCGGTGGTAGCACATACTACGCAGACTCCGTGAAGGGCCGATTCACCATCTCCAGAGACAATTCCAAGAACACGCTGTATCTTCAAATGAACAGCCTGAGAGCTGAGGACACGGCTGTGTATTACTGTGCGAGATCTATAGCAGCAGCCGACTACTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG", "duplicates": [[], [], [], [], []], "v_3p_del": 2, "d_5p_del": 3, "d_3p_del": 6, "j_5p_del": 8, "v_5p_del": 0, "j_3p_del": 0, "vd_insertion": "TC", "dj_insertion": "C", "fv_insertion": "", "jf_insertion": "", "mutated_invariants": [false, false, false, false, false], "in_frames": [true, true, true, true, true], "stops": [true, true, false, true, true], "loci": ["igh", "igh", "igh", "igh", "igh"], "codon_positions": {"v": 282, "j": 312}}, {"qr_gap_seqs": ["", ""], "gl_gap_seqs": ["", ""], "indel_reversed_seqs": ["", ""], "reco_id": "a5090d8abc", "tree": "[&R] ((3d5e18cedd:0.03618649470594946,a834c46736:0.03618649470594946)twz:0.24639847537602985)cqu:0.0;\n", "unique_ids": ["3d5e18cedd", "a834c46736"], "invalid": false, "v_gene": "IGHV4-4*09", "d_gene": "IGHD6-13*01", "j_gene": "IGHJ4*02", "cdr3_length": 48, "mut_freqs": [0.27977839335180055, 0.29362880886426596], "n_mutations": [101, 106], "input_seqs": ["CAGGCGCATCTCCGCTAGTCGGGCCCAATTCTGGTAAATCCTGCGGAGACTCTATCCACCATCCGCACTGTTTCTCGGCGCTCCTTCAGTTGTTGCTACTGGCGTTGACTCCTCCAGCCCCGAGCCAACGCATTTGACTGGATCGAGTACTTTTGTGGCCGTGCCATCACTAAGTACAGCGTCAGCCCCAGGACTCGGTTTGACGAATGAGTTCATAAGTCCATAAGCCATTTCTCGGCGCAGTTGAGGTCTCTGACCACCCCAAACACGGCTGTGTATTACTGTGCGAGGTATTTGCCCGGGGCTAGCAGCGAAGTCTCTGTCTACTGGGGCCAGAGGACCCTGGTCATCGTCATCTCAC", "CCAGCGCATCTCCACTAGTCGCGCCCAATTCTGGTAAATCTTCCGGAGACTCTCTCCCCCATCCGCACTGTTTCTGGGGGCTCCATCAGTTGTCGCTACTGGCGTTGACTCCTCCAACCCCGAGCCAACGCATTTGATTGGATCGGGTACTTTTGTGACCGTGCCATCACCAAGTACAGCGTCAGTCCCAGGACTCGGTTTGACGAATGAGTTCATAAATCCATGAACCAATTCACGCCGCGCTTGAGGTCTCTGACCACCCCAAACTCGGCTGTGTATTACTGTGCGAGGTATTTGCCCGGTGGTAGCAGTGAAGACTCTGCCTGCTGGGGCCGGAGGACCCTGGTCACCGTCATCTCAG"], "has_shm_indels": [false, false], "naive_seq": "CAGGTGCAGCTGCAGGAGTCGGGCCCAGGACTGGTGAAGCCTTCGGAGACCCTGTCCCTCACCTGCACTGTCTCTGGTGGCTCCATCAGTAGTTACTACTGGAGCTGGATCCGGCAGCCCCCAGGGAAGGGACTGGAGTGGATTGGGTACATCTATACCAGTGGGAGCACCAACTACAACCCCTCCCTCAAGAGTCGAGTCACCATATCAGTAGACACGTCCAAGAACCAGTTCTCCCTGAAGCTGAGCTCTGTGACCGCCGCAGACACGGCCGTGTATTACTGTGCGAGTTATTTGCTCGGGTATAGCAGCAGAGCCCCTGTCTACTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG", "duplicates": [[], []], "v_3p_del": 3, "d_5p_del": 0, "d_3p_del": 7, "j_5p_del": 10, "v_5p_del": 0, "j_3p_del": 0, "vd_insertion": "TTATTTGCTC", "dj_insertion": "AGCCCCTGT", "fv_insertion": "", "jf_insertion": "", "mutated_invariants": [false, false], "in_frames": [true, true], "stops": [true, true], "loci": ["igh", "igh"], "codon_positions": {"v": 282, "j": 327}}, {"qr_gap_seqs": ["", "", "", "", "", "CAGGTTCAGCTCGTGCAGTCTGGAGCTGAGGTGAAGAAGCCTGGGGCCTCAGTGAAGGTCTCCTGCAAGGCTTCTGGTTACACCTTTACCAGCTATGGTATCAGCTGGGTGCGACAGGCCCCTGGACAAGGGCTTGAGTGGATGGGATGGATCAGCGCTTACAATGGTAACACAAACTATGCACAGAAGCTCCAGGGCAGAGTCACCATGACCACAGACACATCCACGAGCACAGCCTACATGGAGCTAAGCTGTGAGGAGCCTGAGATCTGACGACACGGCCGTGTATTACTGTGCGAGAGACCCCTCGCAGTATAGCAGCAGCTTCCCTTTTGACTACTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG", "CAGGTTCAGCTCGTGCAGTCTGGAGCTGAGGTGAAGAAGCCTGGGGCCTCAGTGAAGGTCTCCTGCAAGGGACCTTCTGGTTACACCTTTACCAGCTATGGTATCAGCTGGGTGCGACAGGCCCCTGGACAAGGGCTTGAGTGGATGGGATGGATCAGCGCTTACAATGGTAACACAAACTATGCACAGAAGCTCCAGGGCAGAGTCACCATGACCACAGACACATCCACGAGCACAGCCTACATGGAGCTGAGGAGCCTGAGATCTGACGACACGGCCGTGTATTACTGTGCGAGAGACCCCTCGCAGTATAGCAGCAGCTTCCCTTTTGACTACTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG", "", "CAGGTTCAGCTGGTGCAGTCTGGAGCTGTGGTGAAGAAGCCTGGGGCCTCAGTGAAGGTCTCCTGCAAGGCTTCTGGTTACACCTTTACCAGCTATGGTATCAGCTGGGTGCGACAGGCCCCTGGACAAGGGCTTGAGTGGATGGGATGGATCAGCGCTTACAATGGTAACACAAACTATGCACAGAAGCTCCAGGGCAGAGTCACCATGACCACAGACAC....ACGAGCACAGCCTACATGGAGCTGAGGAGCCTGAGATCTGACGACACGGCCGTGTATTACTGTGCGAGAGACCCCTCGCAGTATAGCAGCAGCTTCCCTTTTGACTACTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG", "", ""], "gl_gap_seqs": ["", "", "", "", "", "CAGGTTCAGCTGGTGCAGTCTGGAGCTGAGGTGAAGAAGCCTGGGGCCTCAGTGAAGGTCTCCTGCAAGGCTTCTGGTTACACCTTTACCAGCTATGGTATCAGCTGGGTGCGACAGGCCCCTGGACAAGGGCTTGAGTGGATGGGATGGATCAGCGCTTACAATGGTAACACAAACTATGCACAGAAGCTCCAGGGCAGAGTCACCATGACCACAGACACATCCACGAGCACAGCCTACATGGAGCT.......GAGGAGCCTGAGATCTGACGACACGGCCGTGTATTACTGTGCGAGAGACCCCTCGCAGTATAGCAGCAGCTTCCCTTTTGACTACTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG", "CAGGTTCAGCTGGTGCAGTCTGGAGCTGAGGTGAAGAAGCCTGGGGCCTCAGTGAAGGTCTCCTGCAAGG...CTTCTGGTTACACCTTTACCAGCTATGGTATCAGCTGGGTGCGACAGGCCCCTGGACAAGGGCTTGAGTGGATGGGATGGATCAGCGCTTACAATGGTAACACAAACTATGCACAGAAGCTCCAGGGCAGAGTCACCATGACCACAGACACATCCACGAGCACAGCCTACATGGAGCTGAGGAGCCTGAGATCTGACGACACGGCCGTGTATTACTGTGCGAGAGACCCCTCGCAGTATAGCAGCAGCTTCCCTTTTGACTACTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG", "", "CAGGTTCAGCTGGTGCAGTCTGGAGCTGAGGTGAAGAAGCCTGGGGCCTCAGTGAAGGTCTCCTGCAAGGCTTCTGGTTACACCTTTACCAGCTATGGTATCAGCTGGGTGCGACAGGCCCCTGGACAAGGGCTTGAGTGGATGGGATGGATCAGCGCTTACAATGGTAACACAAACTATGCACAGAAGCTCCAGGGCAGAGTCACCATGACCACAGACACATCCACGAGCACAGCCTACATGGAGCTGAGGAGCCTGAGATCTGACGACACGGCCGTGTATTACTGTGCGAGAGACCCCTCGCAGTATAGCAGCAGCTTCCCTTTTGACTACTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG", "", ""], "indel_reversed_seqs": ["", "", "", "", "", "CAGGTTCAGCTCGTGCAGTCTGGAGCTGAGGTGAAGAAGCCTGGGGCCTCAGTGAAGGTCTCCTGCAAGGCTTCTGGTTACACCTTTACCAGCTATGGTATCAGCTGGGTGCGACAGGCCCCTGGACAAGGGCTTGAGTGGATGGGATGGATCAGCGCTTACAATGGTAACACAAACTATGCACAGAAGCTCCAGGGCAGAGTCACCATGACCACAGACACATCCACGAGCACAGCCTACATGGAGCTGAGGAGCCTGAGATCTGACGACACGGCCGTGTATTACTGTGCGAGAGACCCCTCGCAGTATAGCAGCAGCTTCCCTTTTGACTACTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG", "CAGGTTCAGCTCGTGCAGTCTGGAGCTGAGGTGAAGAAGCCTGGGGCCTCAGTGAAGGTCTCCTGCAAGGCTTCTGGTTACACCTTTACCAGCTATGGTATCAGCTGGGTGCGACAGGCCCCTGGACAAGGGCTTGAGTGGATGGGATGGATCAGCGCTTACAATGGTAACACAAACTATGCACAGAAGCTCCAGGGCAGAGTCACCATGACCACAGACACATCCACGAGCACAGCCTACATGGAGCTGAGGAGCCTGAGATCTGACGACACGGCCGTGTATTACTGTGCGAGAGACCCCTCGCAGTATAGCAGCAGCTTCCCTTTTGACTACTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG", "", "CAGGTTCAGCTGGTGCAGTCTGGAGCTGTGGTGAAGAAGCCTGGGGCCTCAGTGAAGGTCTCCTGCAAGGCTTCTGGTTACACCTTTACCAGCTATGGTATCAGCTGGGTGCGACAGGCCCCTGGACAAGGGCTTGAGTGGATGGGATGGATCAGCGCTTACAATGGTAACACAAACTATGCACAGAAGCTCCAGGGCAGAGTCACCATGACCACAGACACATCCACGAGCACAGCCTACATGGAGCTGAGGAGCCTGAGATCTGACGACACGGCCGTGTATTACTGTGCGAGAGACCCCTCGCAGTATAGCAGCAGCTTCCCTTTTGACTACTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG", "", ""], "reco_id": "9dacfa8deb", "tree": "[&R] (((7c7e2d39ac:0.002267255717234332,(651dbac867:0.001822892856441509,((3f6a0e8f92:0.0016325905543154427,(22ffeb5acc:0.0008038234346451139,(c922857e00:6.522149754976223e-05,cf0720f18a:6.522149754976223e-05)cmq:0.0007386019370953517)hty:0.0008287671196703288)bcq:3.4754822323053916e-05,83a311c688:0.0016673453765793994)cgu:0.00015554747982271159)dtz:0.0004443628613837972)bik:9.741155214377678e-05,((35820aac9c:0.001693591155580496,e783280f21:0.001693591155580496)mvz:0.0006296482431437281,(5f4c456471:0.0012782561049759244,fed0b82e9c:0.0012782561049759244)anv:0.001044983293551308)swx:4.142787130395654e-05)kqu:0.0002855121660787325)evz:0.0;\n", "unique_ids": ["5f4c456471", "651dbac867", "22ffeb5acc", "3f6a0e8f92", "35820aac9c", "cf0720f18a", "83a311c688", "c922857e00", "e783280f21", "fed0b82e9c", "7c7e2d39ac"], "invalid": false, "v_gene": "IGHV1-18*01", "d_gene": "IGHD6-13*01", "j_gene": "IGHJ4*02", "cdr3_length": 51, "mut_freqs": [0.0027247956403269754, 0.008174386920980926, 0.0027247956403269754, 0.0027247956403269754, 0.0027247956403269754, 0.0027247956403269754, 0.0027247956403269754, 0.0027247956403269754, 0.0027247956403269754, 0.0, 0.0], "n_mutations": [1, 3, 1, 1, 1, 1, 1, 1, 1, 0, 0], "input_seqs": ["CAGGTTCAGCTGGTGCAGTCTGGAGCTGAGGTGAAGAAGCCTGGGGCCTCAGTGAAGGTCTCCTGCAAGGCTTCTGGTTACACCTTTACCAGCTATGGTATCAGCTGGGTGCGACAGGCCCCTGGACAAGGGCTTGAGTGGATGGGATGGATCAGCGCTTACAATGGTAACACAAACTATGCACAGAAGCTCCAGGGCAGAGTCACCATGACCACAGACACATCCACGAGCACAGCCTACATGGAGCTGAGGAGCCTGAGATCTGACGACACGGCCGTGTATTACTGTGCGAGAGACCCCTCGCAGTATAGCAGGAGCTTCCCTTTTGACTACTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG", "CAGGTTCAGCTCGTGCAGTCTGGAGCTGAGGTGAAGAAGCCTGGGGCCTCAGTGAAGGTCTCCTGCAAGGCTTCTGGTTACACCTTTACCAGCTATGGTATCAGCTGGGTGCGACAGGCCCCTGGACAAGGGCTTGAGTGGATGGGGTGGATCAGCGCTTACAATGGTAACACAAACTATGCACAGAAGCTCCAGGGCAGAGTCACCATGACCACAGACACATCCACGAGCACAGCCTACATGGAGCTGAGGAGCCTGAGATCTGACGACACGGCCGTGTATTACTGTGCGAGAGACCCCTCGCAGTATAGCAGCAGCTTCCCTTTTGACTACTGGGGCCAGGGAACCCTGATCACCGTCTCCTCAG", "CAGGTTCAGCTCGTGCAGTCTGGAGCTGAGGTGAAGAAGCCTGGGGCCTCAGTGAAGGTCTCCTGCAAGGCTTCTGGTTACACCTTTACCAGCTATGGTATCAGCTGGGTGCGACAGGCCCCTGGACAAGGGCTTGAGTGGATGGGATGGATCAGCGCTTACAATGGTAACACAAACTATGCACAGAAGCTCCAGGGCAGAGTCACCATGACCACAGACACATCCACGAGCACAGCCTACATGGAGCTGAGGAGCCTGAGATCTGACGACACGGCCGTGTATTACTGTGCGAGAGACCCCTCGCAGTATAGCAGCAGCTTCCCTTTTGACTACTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG", "CAGGTTCAGCTCGTGCAGTCTGGAGCTGAGGTGAAGAAGCCTGGGGCCTCAGTGAAGGTCTCCTGCAAGGCTTCTGGTTACACCTTTACCAGCTATGGTATCAGCTGGGTGCGACAGGCCCCTGGACAAGGGCTTGAGTGGATGGGATGGATCAGCGCTTACAATGGTAACACAAACTATGCACAGAAGCTCCAGGGCAGAGTCACCATGACCACAGACACATCCACGAGCACAGCCTACATGGAGCTGAGGAGCCTGAGATCTGACGACACGGCCGTGTATTACTGTGCGAGAGACCCCTCGCAGTATAGCAGCAGCTTCCCTTTTGACTACTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG", "CAGGTTCAGCTGGTGCAGTCTGGAGCTGAGGTGAAGAAGCCTGGGGCCTCAGTGAAGGTCTCCTGCAAGGCTTCTGGTTACACCTTTACCAGCTATGGTATCAGCTGGGTGCGACGGGCCCCTGGACAAGGGCTTGAGTGGATGGGATGGATCAGCGCTTACAATGGTAACACAAACTATGCACAGAAGCTCCAGGGCAGAGTCACCATGACCACAGACACATCCACGAGCACAGCCTACATGGAGCTGAGGAGCCTGAGATCTGACGACACGGCCGTGTATTACTGTGCGAGAGACCCCTCGCAGTATAGCAGCAGCTTCCCTTTTGACTACTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG", "CAGGTTCAGCTCGTGCAGTCTGGAGCTGAGGTGAAGAAGCCTGGGGCCTCAGTGAAGGTCTCCTGCAAGGCTTCTGGTTACACCTTTACCAGCTATGGTATCAGCTGGGTGCGACAGGCCCCTGGACAAGGGCTTGAGTGGATGGGATGGATCAGCGCTTACAATGGTAACACAAACTATGCACAGAAGCTCCAGGGCAGAGTCACCATGACCACAGACACATCCACGAGCACAGCCTACATGGAGCTAAGCTGTGAGGAGCCTGAGATCTGACGACACGGCCGTGTATTACTGTGCGAGAGACCCCTCGCAGTATAGCAGCAGCTTCCCTTTTGACTACTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG", "CAGGTTCAGCTCGTGCAGTCTGGAGCTGAGGTGAAGAAGCCTGGGGCCTCAGTGAAGGTCTCCTGCAAGGGACCTTCTGGTTACACCTTTACCAGCTATGGTATCAGCTGGGTGCGACAGGCCCCTGGACAAGGGCTTGAGTGGATGGGATGGATCAGCGCTTACAATGGTAACACAAACTATGCACAGAAGCTCCAGGGCAGAGTCACCATGACCACAGACACATCCACGAGCACAGCCTACATGGAGCTGAGGAGCCTGAGATCTGACGACACGGCCGTGTATTACTGTGCGAGAGACCCCTCGCAGTATAGCAGCAGCTTCCCTTTTGACTACTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG", "CAGGTTCAGCTCGTGCAGTCTGGAGCTGAGGTGAAGAAGCCTGGGGCCTCAGTGAAGGTCTCCTGCAAGGCTTCTGGTTACACCTTTACCAGCTATGGTATCAGCTGGGTGCGACAGGCCCCTGGACAAGGGCTTGAGTGGATGGGATGGATCAGCGCTTACAATGGTAACACAAACTATGCACAGAAGCTCCAGGGCAGAGTCACCATGACCACAGACACATCCACGAGCACAGCCTACATGGAGCTGAGGAGCCTGAGATCTGACGACACGGCCGTGTATTACTGTGCGAGAGACCCCTCGCAGTATAGCAGCAGCTTCCCTTTTGACTACTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG", "CAGGTTCAGCTGGTGCAGTCTGGAGCTGTGGTGAAGAAGCCTGGGGCCTCAGTGAAGGTCTCCTGCAAGGCTTCTGGTTACACCTTTACCAGCTATGGTATCAGCTGGGTGCGACAGGCCCCTGGACAAGGGCTTGAGTGGATGGGATGGATCAGCGCTTACAATGGTAACACAAACTATGCACAGAAGCTCCAGGGCAGAGTCACCATGACCACAGACACACGAGCACAGCCTACATGGAGCTGAGGAGCCTGAGATCTGACGACACGGCCGTGTATTACTGTGCGAGAGACCCCTCGCAGTATAGCAGCAGCTTCCCTTTTGACTACTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG", "CAGGTTCAGCTGGTGCAGTCTGGAGCTGAGGTGAAGAAGCCTGGGGCCTCAGTGAAGGTCTCCTGCAAGGCTTCTGGTTACACCTTTACCAGCTATGGTATCAGCTGGGTGCGACAGGCCCCTGGACAAGGGCTTGAGTGGATGGGATGGATCAGCGCTTACAATGGTAACACAAACTATGCACAGAAGCTCCAGGGCAGAGTCACCATGACCACAGACACATCCACGAGCACAGCCTACATGGAGCTGAGGAGCCTGAGATCTGACGACACGGCCGTGTATTACTGTGCGAGAGACCCCTCGCAGTATAGCAGCAGCTTCCCTTTTGACTACTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG", "CAGGTTCAGCTGGTGCAGTCTGGAGCTGAGGTGAAGAAGCCTGGGGCCTCAGTGAAGGTCTCCTGCAAGGCTTCTGGTTACACCTTTACCAGCTATGGTATCAGCTGGGTGCGACAGGCCCCTGGACAAGGGCTTGAGTGGATGGGATGGATCAGCGCTTACAATGGTAACACAAACTATGCACAGAAGCTCCAGGGCAGAGTCACCATGACCACAGACACATCCACGAGCACAGCCTACATGGAGCTGAGGAGCCTGAGATCTGACGACACGGCCGTGTATTACTGTGCGAGAGACCCCTCGCAGTATAGCAGCAGCTTCCCTTTTGACTACTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG"], "has_shm_indels": [false, false, false, false, false, true, true, false, true, false, false], "naive_seq": "CAGGTTCAGCTGGTGCAGTCTGGAGCTGAGGTGAAGAAGCCTGGGGCCTCAGTGAAGGTCTCCTGCAAGGCTTCTGGTTACACCTTTACCAGCTATGGTATCAGCTGGGTGCGACAGGCCCCTGGACAAGGGCTTGAGTGGATGGGATGGATCAGCGCTTACAATGGTAACACAAACTATGCACAGAAGCTCCAGGGCAGAGTCACCATGACCACAGACACATCCACGAGCACAGCCTACATGGAGCTGAGGAGCCTGAGATCTGACGACACGGCCGTGTATTACTGTGCGAGAGACCCCTCGCAGTATAGCAGCAGCTTCCCTTTTGACTACTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG", "duplicates": [[], [], [], [], [], [], [], [], [], [], []], "v_3p_del": 0, "d_5p_del": 2, "d_3p_del": 7, "j_5p_del": 6, "v_5p_del": 0, "j_3p_del": 0, "vd_insertion": "CCCCTCGCA", "dj_insertion": "CTTCCCTT", "fv_insertion": "", "jf_insertion": "", "mutated_invariants": [false, false, false, false, false, false, false, false, false, false, false], "in_frames": [true, true, true, true, true, false, true, true, false, true, true], "stops": [false, false, false, false, false, true, false, false, true, false, false], "loci": ["igh", "igh", "igh", "igh", "igh", "igh", "igh", "igh", "igh", "igh", "igh"], "codon_positions": {"v": 285, "j": 333}}, {"qr_gap_seqs": ["", "", "", "GAGGTGCAGCTGTTGGAGTCTGGGGGAGGCTTGGTACAGCCTGGGGGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCTTTGGCAGCTATGCCATGCGCTGGGTCCGCCAGGCTCCAGAGAAGGGGCTGGAGTGGGTCTCAGCTATTAGTGGTAGTGGTGG.......TACTACGCAGACTCCGTGAAGGGCCGGTTCACCATCTCCAGAGACAATTCCAAGAAAACGCTGTATCTGCAAATGAACAGCCTGAGAGCCGAGGACACGGCCGTATATTACTGTGCGAAAGAATTGCGTTTGGGGGAGTTATCGTTAT.CCCCTTTGACTACTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG"], "gl_gap_seqs": ["", "", "", "GAGGTGCAGCTGTTGGAGTCTGGGGGAGGCTTGGTACAGCCTGGGGGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCTTTAGCAGCTATGCCATGAGCTGGGTCCGCCAGGCTCCAGGGAAGGGGCTGGAGTGGGTCTCAGCTATTAGTGGTAGTGGTGGTAGCACATACTACGCAGACTCCGTGAAGGGCCGGTTCACCATCTCCAGAGACAATTCCAAGAACACGCTGTATCTGCAAATGAACAGCCTGAGAGCCGAGGACACGGCCGTATATTACTGTGCGAAAGAATTACGTTTGGGGGAGTTATCGTTATACCCCTTTGACTACTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG"], "indel_reversed_seqs": ["", "", "", "GAGGTGCAGCTGTTGGAGTCTGGGGGAGGCTTGGTACAGCCTGGGGGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCTTTGGCAGCTATGCCATGCGCTGGGTCCGCCAGGCTCCAGAGAAGGGGCTGGAGTGGGTCTCAGCTATTAGTGGTAGTGGTGGTAGCACATACTACGCAGACTCCGTGAAGGGCCGGTTCACCATCTCCAGAGACAATTCCAAGAAAACGCTGTATCTGCAAATGAACAGCCTGAGAGCCGAGGACACGGCCGTATATTACTGTGCGAAAGAATTGCGTTTGGGGGAGTTATCGTTATACCCCTTTGACTACTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG"], "reco_id": "f220c52535", "tree": "[&R] ((3cd1599613:0.015251980243404,((d76f52b01a:0.007461516959039839,0b027c31ea:0.007461516959039839)pqs:0.004118786935817008,a32918fa7c:0.011580303889941666)kmw:0.003671676348547156)hmq:0.0007914122438129608)afh:0.0;\n", "unique_ids": ["a32918fa7c", "d76f52b01a", "0b027c31ea", "3cd1599613"], "invalid": false, "v_gene": "IGHV3-23*01", "d_gene": "IGHD3-16*02", "j_gene": "IGHJ4*02", "cdr3_length": 54, "mut_freqs": [0.013513513513513514, 0.021621621621621623, 0.013513513513513514, 0.013513513513513514], "n_mutations": [5, 8, 5, 5], "input_seqs": ["GAGGTGCAGCTGTTGGAGTCTGGGGGAGGCTTGGTACAGCCTGGGGGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCTTTAGCAGCTATGCCATGAGCTGGGTCCGCCAGGCTCCAGGGAAGGGCCTGGAGTGGGTCTCAGCTATTAGTGGTAGTGGTGGTAGCACATACTACGCAGACTCCGTGAAGCGCCGGTTCACCATCTCCAGAGACAATTCCAAGAACACGGTGTATCTGCAAATGAACAGCCTGAGAGCCGAGGACACGGCCGTATATTACTGTGCGAAAGAATTACGTTTGCGGGAGTTATCGTTATACCCCTTTGTCTACTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG", "GAGGTGCAGCTGTTGGAGTCTGGGGGGGGCTTGGTACAGCCTGGGGGGTCCCTGAGACTCTCCTGTCCAGCCTCTGGATTCACCTTTAGCAGCTATGCCATGACCTGGGTCCGCCAGGCTCCAGGGAAGGGGCTGGAGTGGGTCTCAGCTATTAGTGGTAGTGGTGGTAGCACATACTACGCAGACTCCGTGAAGCGCCGGTTCACCATCTCCAGAGACAATTCCAAGAACACGCTGTATCTGCAAATGAACAGCCTGAGAGCCGAGGACACGGCCGTATATTACTGTGCGGAAGAATTACGTTTGCGAGAGTTATCGTTATACCCCTTTGACTTCTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG", "GAGGTGCAGCTGTTGGAGTCTGGGGGGGGCTTGGTACAGCCTGGGGGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCTTTAGCAGCTATGCCACGAGCTGGGTCCGCCAGGCTCCAGGGAAGGGGCTGGAGTGGGTCTCAGCTATTAGTGGTAGTGGTGGTAGCACATACTACGCAGACTCCGTGAAGCGCCGGTTCACCATCTCCAGAGACAATTCCAAGAACACGCTGTATCTGCAAATGAACAGCCTGAGAGCCGAGGACACGGCCGTATATTACTGTGCGAAAGAATTACGTTTGCGGGAGTTATCGTTATACCCCTTTGACTTCTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG", "GAGGTGCAGCTGTTGGAGTCTGGGGGAGGCTTGGTACAGCCTGGGGGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCTTTGGCAGCTATGCCATGCGCTGGGTCCGCCAGGCTCCAGAGAAGGGGCTGGAGTGGGTCTCAGCTATTAGTGGTAGTGGTGGTACTACGCAGACTCCGTGAAGGGCCGGTTCACCATCTCCAGAGACAATTCCAAGAAAACGCTGTATCTGCAAATGAACAGCCTGAGAGCCGAGGACACGGCCGTATATTACTGTGCGAAAGAATTGCGTTTGGGGGAGTTATCGTTATCCCCTTTGACTACTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG"], "has_shm_indels": [false, false, false, true], "naive_seq": "GAGGTGCAGCTGTTGGAGTCTGGGGGAGGCTTGGTACAGCCTGGGGGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCTTTAGCAGCTATGCCATGAGCTGGGTCCGCCAGGCTCCAGGGAAGGGGCTGGAGTGGGTCTCAGCTATTAGTGGTAGTGGTGGTAGCACATACTACGCAGACTCCGTGAAGGGCCGGTTCACCATCTCCAGAGACAATTCCAAGAACACGCTGTATCTGCAAATGAACAGCCTGAGAGCCGAGGACACGGCCGTATATTACTGTGCGAAAGAATTACGTTTGGGGGAGTTATCGTTATACCCCTTTGACTACTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG", "duplicates": [[], [], [], []], "v_3p_del": 0, "d_5p_del": 8, "d_3p_del": 0, "j_5p_del": 4, "v_5p_del": 0, "j_3p_del": 0, "vd_insertion": "", "dj_insertion": "C", "fv_insertion": "", "jf_insertion": "", "mutated_invariants": [false, false, false, false], "in_frames": [true, true, true, false], "stops": [false, false, false, true], "loci": ["igh", "igh", "igh", "igh"], "codon_positions": {"v": 285, "j": 336}}, {"qr_gap_seqs": ["", "CAGGTGCAGCTGCACGAGTCGGGCCCAGGACTGGTGAAGCCTTCGGAGACCCTGT.......CTGCACTGTCTCTGGTGGCTCCGTCAGCAGTGGTAGTTACTACTGGAGCTGGATCCGGCAGCCCCCAGGGAAGGGACTGGACTGGATTGGGTATATCTATTACAGTGGGAGCACCAACTACAACCCCTCCCTCGAGAGTCGAGTCACCATATCAGTAGACACGTCCAAGAACCAGTTCTTCCTGAAGCTGAGCTCTGTGACCGCTGCGGACACGGCCCTGTATTACTGTGCGAGAGAGTATCGCTATGG.....GTGGTTATTACTACGAATACTTCCAGCACTGGGGCCAGGGCACCCTGGTCACCGTCTCCTCAG", "", "CAGGTGCAGCTGCAGGAGTCGGGCCCAGGACTGGTGAAGCCTTCGGAGACCCTGTCCCTCACCTGCGCTGTCTCTGGTGGCTCCGTCAGCAGTGGTAGTTACTACTGGAGCTGGATCCGGCAGCCCCCAGGGAAGGGACTGGAGTGGATTGGGTATATCTATTACAGTGGGAGCACCAACTACAACCCCTCCCTCAAGAGTCGAGTCACCATATCAGTAGACACGTCCAAGAACCA............GCTGAGCTCTGTGACCGCTGCGGACACGGCCGTGTATTACTGTGCGACAGAGTATTACTATGATAGTAGTGGTTATTACTACGAATACTTCATTCCAGCACTGGGGCCAGGGCACCCTGGTCACCGTCTCCTCAG", "", "", "", "", "", "", "", "", "", "", "CAGGTGCAGCTGGTCTGAATGTGCAATGGTCCTAAACAGGAGTCGGGCCCAGCACTGGTGAAGCCTTCGGAGACCCTGTCCCTCACCTGCACTGTCTCTGGTGGCTCCGTCAGCAGTGGTAGTTACTACTGGAGCTGGATCCGGCAGCCCCCAGGGAAGGGACTGGAGTGGATTGGGTATATCTATTACAGTGGGAGCACCAACTACAACCCCTCCCTCAAGAGTCGAGTCACCATATCAGTAGACACGTCCAAGAACCAGTTCTCCCTGAAGCTGAGCTCTGTGACCGCTGCGGACACGGCCGTGTATTACTGTGCGAGAGAGTATTACTATGATAGTAGTGGTTATTACTACGAATACTTCCAGCACTGGCGCCAGGGCACCCTGGTCACCGTCTCCTCAG", "", "CAGGTGCAGCTGCAGGAGTCGGGCCCAGGACTGGTGAAGCCTTCGGAGACCCTGTCCCTCACCTGCACTGTCTCTGGTGGCTCCGTCAACAGTGGTAGTTACTCACTGGAGCTGGATCCGGCAGCCCCCAGGGAAGGGACTGGACTGGATTGGGTATATCTATTACAGTGGGAGCACCAACTACAACCCCTCCCTCAAGAGTCGAGTCACCATATCAGTAGACACGTCCAAGAACCAGTTCTTCCTGAAGCTGAGCTCTGTGACCGCTGCGGACACGGCCCTGTATTACTGTGCGAGAGAGTATCGCTATGGTAGTAGTGGTTATTACTACGAATACTTCCAGCACTGGGGCCAGGGCACCCTGGTCACCGTCTCCCCAG", "", "CAGGTGCAGCTGCAGGAGTCGGGCCCAGGACTGGTGAAGCCTTCGGAGACCCTGTCCCTCACCTGCACTGTCTCTGGTGGCTCCGTCAGCAGTGGTAGTTACTACTGGAGCTGGATCCGGCAGCCCCCAGGGAAGGGACTGGAGTGGATTGGGTATATCTATTACAGTGGGAGCACCAACATACAACCCCTCCTTCAAGAGTCGAGTCACCATATCAGTAGACGCGTCCAAGAACCAGTTCTCCCTGAAGCTGAGCTCTGTGACCGCTGCGGACACGGCCGTGTATTACTGTGCGAGAGAGTATTACTATGATAGTAGTGGTTATTACTACGAATACTTCCAGCACTGGGGCCAGGACACCCTGGTCACCGTCTCCTCAG", "", "", ""], "gl_gap_seqs": ["", "CAGGTGCAGCTGCAGGAGTCGGGCCCAGGACTGGTGAAGCCTTCGGAGACCCTGTCCCTCACCTGCACTGTCTCTGGTGGCTCCGTCAGCAGTGGTAGTTACTACTGGAGCTGGATCCGGCAGCCCCCAGGGAAGGGACTGGAGTGGATTGGGTATATCTATTACAGTGGGAGCACCAACTACAACCCCTCCCTCAAGAGTCGAGTCACCATATCAGTAGACACGTCCAAGAACCAGTTCTCCCTGAAGCTGAGCTCTGTGACCGCTGCGGACACGGCCGTGTATTACTGTGCGAGAGAGTATTACTATGATAGTAGTGGTTATTACTACGAATACTTCCAGCACTGGGGCCAGGGCACCCTGGTCACCGTCTCCTCAG", "", "CAGGTGCAGCTGCAGGAGTCGGGCCCAGGACTGGTGAAGCCTTCGGAGACCCTGTCCCTCACCTGCACTGTCTCTGGTGGCTCCGTCAGCAGTGGTAGTTACTACTGGAGCTGGATCCGGCAGCCCCCAGGGAAGGGACTGGAGTGGATTGGGTATATCTATTACAGTGGGAGCACCAACTACAACCCCTCCCTCAAGAGTCGAGTCACCATATCAGTAGACACGTCCAAGAACCAGTTCTCCCTGAAGCTGAGCTCTGTGACCGCTGCGGACACGGCCGTGTATTACTGTGCGAGAGAGTATTACTATGATAGTAGTGGTTATTACTACGAATACTT....CCAGCACTGGGGCCAGGGCACCCTGGTCACCGTCTCCTCAG", "", "", "", "", "", "", "", "", "", "", "CAGGTGCAGCTG........................CAGGAGTCGGGCCCAGGACTGGTGAAGCCTTCGGAGACCCTGTCCCTCACCTGCACTGTCTCTGGTGGCTCCGTCAGCAGTGGTAGTTACTACTGGAGCTGGATCCGGCAGCCCCCAGGGAAGGGACTGGAGTGGATTGGGTATATCTATTACAGTGGGAGCACCAACTACAACCCCTCCCTCAAGAGTCGAGTCACCATATCAGTAGACACGTCCAAGAACCAGTTCTCCCTGAAGCTGAGCTCTGTGACCGCTGCGGACACGGCCGTGTATTACTGTGCGAGAGAGTATTACTATGATAGTAGTGGTTATTACTACGAATACTTCCAGCACTGGGGCCAGGGCACCCTGGTCACCGTCTCCTCAG", "", "CAGGTGCAGCTGCAGGAGTCGGGCCCAGGACTGGTGAAGCCTTCGGAGACCCTGTCCCTCACCTGCACTGTCTCTGGTGGCTCCGTCAGCAGTGGTAGTTACT.ACTGGAGCTGGATCCGGCAGCCCCCAGGGAAGGGACTGGAGTGGATTGGGTATATCTATTACAGTGGGAGCACCAACTACAACCCCTCCCTCAAGAGTCGAGTCACCATATCAGTAGACACGTCCAAGAACCAGTTCTCCCTGAAGCTGAGCTCTGTGACCGCTGCGGACACGGCCGTGTATTACTGTGCGAGAGAGTATTACTATGATAGTAGTGGTTATTACTACGAATACTTCCAGCACTGGGGCCAGGGCACCCTGGTCACCGTCTCCTCAG", "", "CAGGTGCAGCTGCAGGAGTCGGGCCCAGGACTGGTGAAGCCTTCGGAGACCCTGTCCCTCACCTGCACTGTCTCTGGTGGCTCCGTCAGCAGTGGTAGTTACTACTGGAGCTGGATCCGGCAGCCCCCAGGGAAGGGACTGGAGTGGATTGGGTATATCTATTACAGTGGGAGCACCAAC.TACAACCCCTCCCTCAAGAGTCGAGTCACCATATCAGTAGACACGTCCAAGAACCAGTTCTCCCTGAAGCTGAGCTCTGTGACCGCTGCGGACACGGCCGTGTATTACTGTGCGAGAGAGTATTACTATGATAGTAGTGGTTATTACTACGAATACTTCCAGCACTGGGGCCAGGGCACCCTGGTCACCGTCTCCTCAG", "", "", ""], "indel_reversed_seqs": ["", "CAGGTGCAGCTGCACGAGTCGGGCCCAGGACTGGTGAAGCCTTCGGAGACCCTGTCCCTCACCTGCACTGTCTCTGGTGGCTCCGTCAGCAGTGGTAGTTACTACTGGAGCTGGATCCGGCAGCCCCCAGGGAAGGGACTGGACTGGATTGGGTATATCTATTACAGTGGGAGCACCAACTACAACCCCTCCCTCGAGAGTCGAGTCACCATATCAGTAGACACGTCCAAGAACCAGTTCTTCCTGAAGCTGAGCTCTGTGACCGCTGCGGACACGGCCCTGTATTACTGTGCGAGAGAGTATCGCTATGGTAGTAGTGGTTATTACTACGAATACTTCCAGCACTGGGGCCAGGGCACCCTGGTCACCGTCTCCTCAG", "", "CAGGTGCAGCTGCAGGAGTCGGGCCCAGGACTGGTGAAGCCTTCGGAGACCCTGTCCCTCACCTGCGCTGTCTCTGGTGGCTCCGTCAGCAGTGGTAGTTACTACTGGAGCTGGATCCGGCAGCCCCCAGGGAAGGGACTGGAGTGGATTGGGTATATCTATTACAGTGGGAGCACCAACTACAACCCCTCCCTCAAGAGTCGAGTCACCATATCAGTAGACACGTCCAAGAACCAGTTCTCCCTGAAGCTGAGCTCTGTGACCGCTGCGGACACGGCCGTGTATTACTGTGCGACAGAGTATTACTATGATAGTAGTGGTTATTACTACGAATACTTCCAGCACTGGGGCCAGGGCACCCTGGTCACCGTCTCCTCAG", "", "", "", "", "", "", "", "", "", "", "CAGGTGCAGCTGCAGGAGTCGGGCCCAGCACTGGTGAAGCCTTCGGAGACCCTGTCCCTCACCTGCACTGTCTCTGGTGGCTCCGTCAGCAGTGGTAGTTACTACTGGAGCTGGATCCGGCAGCCCCCAGGGAAGGGACTGGAGTGGATTGGGTATATCTATTACAGTGGGAGCACCAACTACAACCCCTCCCTCAAGAGTCGAGTCACCATATCAGTAGACACGTCCAAGAACCAGTTCTCCCTGAAGCTGAGCTCTGTGACCGCTGCGGACACGGCCGTGTATTACTGTGCGAGAGAGTATTACTATGATAGTAGTGGTTATTACTACGAATACTTCCAGCACTGGCGCCAGGGCACCCTGGTCACCGTCTCCTCAG", "", "CAGGTGCAGCTGCAGGAGTCGGGCCCAGGACTGGTGAAGCCTTCGGAGACCCTGTCCCTCACCTGCACTGTCTCTGGTGGCTCCGTCAACAGTGGTAGTTACTACTGGAGCTGGATCCGGCAGCCCCCAGGGAAGGGACTGGACTGGATTGGGTATATCTATTACAGTGGGAGCACCAACTACAACCCCTCCCTCAAGAGTCGAGTCACCATATCAGTAGACACGTCCAAGAACCAGTTCTTCCTGAAGCTGAGCTCTGTGACCGCTGCGGACACGGCCCTGTATTACTGTGCGAGAGAGTATCGCTATGGTAGTAGTGGTTATTACTACGAATACTTCCAGCACTGGGGCCAGGGCACCCTGGTCACCGTCTCCCCAG", "", "CAGGTGCAGCTGCAGGAGTCGGGCCCAGGACTGGTGAAGCCTTCGGAGACCCTGTCCCTCACCTGCACTGTCTCTGGTGGCTCCGTCAGCAGTGGTAGTTACTACTGGAGCTGGATCCGGCAGCCCCCAGGGAAGGGACTGGAGTGGATTGGGTATATCTATTACAGTGGGAGCACCAACTACAACCCCTCCTTCAAGAGTCGAGTCACCATATCAGTAGACGCGTCCAAGAACCAGTTCTCCCTGAAGCTGAGCTCTGTGACCGCTGCGGACACGGCCGTGTATTACTGTGCGAGAGAGTATTACTATGATAGTAGTGGTTATTACTACGAATACTTCCAGCACTGGGGCCAGGACACCCTGGTCACCGTCTCCTCAG", "", "", ""], "reco_id": "e19f613502", "tree": "[&R] (((((((((a8a845afd0:0.004530249942342193,79997552ff:0.004530249942342193)hmt:0.00022291260734998608,1fa3a3147c:0.0047531625500090505)dop:0.0007929145155235514,(340e539235:0.0015884440502783258,e45374ef7b:0.0015884440502783258)mnu:0.003957633014462099)lpv:0.003521147738038931,1a680fb189:0.009067224801987179)nvx:0.0002722274825795668,(6be16277dd:0.008051884595028274,((a366840534:0.001510048410011483,64ae95318c:0.001510048410011483)eju:0.0026012372186592614,(49516f50c8:0.0034715838798940646,(5ad57efbb9:0.002530568061476283,aa6e1a8781:0.002530568061476283)ist:0.0009410158184177819)jqz:0.0006397017488558974)bgx:0.00394059896635753)qrt:0.001287567691598131)jvx:0.0005607565295872465,(16caab20bd:0.009677496390756182,(aa7dae44c3:0.008129340134513007,((437bff5b48:0.002346410619402535,25edd0ce47:0.002346410619402535)gov:0.0038922001880019965,7a63383c3f:0.006238610807404532)pxz:0.0018907293247319447)dnq:0.0015481562578275293)blt:0.0002227124256159049)inp:2.6332399451427232e-05,(f6a0022f12:0.0045972621150797395,dc6a919315:0.0045972621150797395)bpt:0.005329279100371452)dln:0.00035986136677147496,((775dc4cd18:0.0016939310887261617,f1712e10a7:0.0016939310887261617)bpx:0.006690758736821443,bb706a907c:0.008384689822378897)bfs:0.0019017127564374089)hop:0.00037097034756984544)lmw:0.0;\n", "unique_ids": ["49516f50c8", "775dc4cd18", "f6a0022f12", "437bff5b48", "a366840534", "6be16277dd", "64ae95318c", "e45374ef7b", "5ad57efbb9", "16caab20bd", "aa6e1a8781", "1a680fb189", "bb706a907c", "aa7dae44c3", "dc6a919315", "25edd0ce47", "f1712e10a7", "1fa3a3147c", "340e539235", "79997552ff", "7a63383c3f", "a8a845afd0"], "invalid": false, "v_gene": "IGHV4-61*01", "d_gene": "IGHD3-22*01", "j_gene": "IGHJ1*01", "cdr3_length": 60, "mut_freqs": [0.0158311345646438, 0.021108179419525065, 0.013192612137203167, 0.005277044854881266, 0.021108179419525065, 0.013192612137203167, 0.018469656992084433, 0.010554089709762533, 0.018469656992084433, 0.0079155672823219, 0.0158311345646438, 0.0079155672823219, 0.002638522427440633, 0.010554089709762533, 0.005277044854881266, 0.010554089709762533, 0.021108179419525065, 0.026385224274406333, 0.0079155672823219, 0.010554089709762533, 0.0079155672823219, 0.0158311345646438], "n_mutations": [6, 8, 5, 2, 8, 5, 7, 4, 7, 3, 6, 3, 1, 4, 2, 4, 8, 10, 3, 4, 3, 6], "input_seqs": ["AAGGTGCCGCTGCAGGAGTCGGGCCCAGGACTGGTGAAGCCTTCGGAGACCCTGTCCCTCACCTGCACTGTCTCTGGTGGTTCCGTCAGCAGTGGTAGTTACTACTGGAGCTGGATCCGGCAGCCCCCAGGGAAGGGACTGGAGTGGATTGGGTATATCTATTACAGTGGGAGCACCAACTACAACCCCTCCCTCAAGAGTCGAGTCACCATATCAGTAGACACGTCCAAGAACCAGTTCTCCCTGAAACTGAGCTCTGTGACCGCTGCGGACACGGCCGTGTATTACTGTGCGAGAGAGTATTACTATGATAGTAGTGGTTATTACTACGAATACTTCCAGCAGTGGGGCCAGGGCACCCTGGTCACCGTCTACTCAG", "CAGGTGCAGCTGCACGAGTCGGGCCCAGGACTGGTGAAGCCTTCGGAGACCCTGTCTGCACTGTCTCTGGTGGCTCCGTCAGCAGTGGTAGTTACTACTGGAGCTGGATCCGGCAGCCCCCAGGGAAGGGACTGGACTGGATTGGGTATATCTATTACAGTGGGAGCACCAACTACAACCCCTCCCTCGAGAGTCGAGTCACCATATCAGTAGACACGTCCAAGAACCAGTTCTTCCTGAAGCTGAGCTCTGTGACCGCTGCGGACACGGCCCTGTATTACTGTGCGAGAGAGTATCGCTATGGGTGGTTATTACTACGAATACTTCCAGCACTGGGGCCAGGGCACCCTGGTCACCGTCTCCTCAG", "CAGGTGCACCTGCAGGAGTCGGGCCCAGGACTGGTTAAGCCTTCGGAGACCCTGTCCCTCACCTGCACTGTCTCTGGTGGCTCCGTCAGCAGTGGTAGTTACTACTGGAGCTGGATCCGGCAGCCCCCAGGGAAGGGACTGGAGTGGATTGGGTATATCTATTACAGTGGGAGCACCAACTACAACCCCTCCCTCAAGAGTCGAGTCACCATATCAGTAGACACGTCCAAGAACCAGTTCTCCCTGAAGCTGAGCTCTGTGACCGCTGCGGACACGGCCGTGTATTACTGTGCGAGAGATTATTACTATGATAGTAGTGGTTATTACTACGAATACTTCCAGCACTGGCGCCAGGGCACCCTGGTCACCGTCTCCTCCG", "CAGGTGCAGCTGCAGGAGTCGGGCCCAGGACTGGTGAAGCCTTCGGAGACCCTGTCCCTCACCTGCGCTGTCTCTGGTGGCTCCGTCAGCAGTGGTAGTTACTACTGGAGCTGGATCCGGCAGCCCCCAGGGAAGGGACTGGAGTGGATTGGGTATATCTATTACAGTGGGAGCACCAACTACAACCCCTCCCTCAAGAGTCGAGTCACCATATCAGTAGACACGTCCAAGAACCAGCTGAGCTCTGTGACCGCTGCGGACACGGCCGTGTATTACTGTGCGACAGAGTATTACTATGATAGTAGTGGTTATTACTACGAATACTTCATTCCAGCACTGGGGCCAGGGCACCCTGGTCACCGTCTCCTCAG", "AAGGTGCAGCTGCAGGAGTCGGGCCCAGGACTGGTGAAGACTTCGGAGACCCTGTCCCTCACCTGCACTGTTTCTGGTGGTTCCGTCAGCAGTGGTAGTTACTACTGGAGCTGGATCCGGCAGCCCCCAGGGAAGGGACTGGAGTGGATTGGGTATATCTATTACAGTGGGAGCACCAACTACAACCCCTCCCTCAAGAGTCGAGTCACCATATCAGTCGACACGTCCAAGAACCAGTTCTCCCTGAAGCTGAGCTCTGTGACCGCTGCGGACACGGCCGTGTATTACTGTGCGAGAGAGTATTACTATGATAGTAGTGGTTATTACTACGAATACTTCCAGCAGTGGGGCCAGGGCACCCTGGTCACCGTATACTCAG", "AAGGTGCAGCTGCAGGAGTCGGGCCCAGGACTGGTGAAGCCTTCGGAGACCCTGTCCCTCACCTGCACTGTCTCTGGTGGTTCCGTCAGCAGTGGTAGTTACTACTGGAGCTGGATCCGGCAGCCCCCAGGGAAGGGACTGGAGTGGATTGGGTATATCTATTACAGTGGGGGCACCAACTACAACCCCTCCCTCAAGAGTCGAGTCACCATATCAGTAGACACGTCCAAGAACCAGTTCTCCCTGAAGCTGAGCTCTGTGACCGCTGCGGACACGGCCGTGTATTACTGTGCGAGGGAGTATTACTATGATAGTAGTGGTTATTACTACGAATACTTCCAGCACTGGGGCCAGGGCACCCTGGTCACCGTCTACTCAG", "AAGGTGCAGCTGCAGGAGTCGGGCCCAGGACTGGTGAAGACTTCGGAGACCCTGTCCCTCACCTGCACTGTCTCTGGTGGTTCCGTCAGCAGTGGTAGTTACTACTGGAGCTGGATCCGGCAGCCCCCAGGGAAGGGACTGGAGTGGATTGGGTATATCTATTACAGTGGGAGCACCAACTACAACCCCTCCCTCAAGAGTCGAGTCACCATATCAGTAGACACGTCCAACAACCAGTTCTCCCTGAAGCTGAGCTCTGTGACCGCTGCGGACACGGCCGTGTATTACTGTGCGAGAGAGTATTACTATGATAGTAGTGGTTATTACTACGAATACTTCCAGCAGTGGGGCCAGGGCACCCTGGTCACCGTATACTCAG", "CAGGTGCAGCTGCAGGAGTCGGGCCCAGGACTGGTGAAGCCTTCGGAGACCCTGTCCCTCACCTGCACTGTCTCTGGTGGCTCCGTCAGCAGTGGTAGTTACTACTGGAGCTGGATCCGGCAGCCCCCAGGGAAGGGACTGGAGTGGATTGGGTATATCTATTACAGTGGGAGCACCAACTACAACCCCTCCTTCAAGAGTCGAGTCACCATATCAGTAGACGCGTCCAAGAACCAGTTCTCCCTGAAGCTGACCTCTGTGACCGCTGCGGACACGGCCGTGTATTACTGTGCGAGAGAGTATTACTATGATAGTAGTGGTTATTACTACGAATACTTCCAGCACTGGGGCCAGGACACCCTGGTCACCGTCTCCTCAG", "AAGGTGCCGCTGCAGGAGTCGGGCCCAGGACTGGTGAAGCCTTCGGAGACCCTGTCCCTCACCTGCACTGTCTCTGGTGGTTCCGTCAACAGTGGTAGTTACTACTGGAGCTGGATCCGGCAGCCCCCAGGGAAGGGACTGGAGTGGATTGGGTATATCTATTACAGTGGGAGCACCAACTACAACCCCTCCCTCAAGAGTCGAGTCACCATATCAGTAGACACGTCTAAGAACCAGTTCTCCCTGAAGCTGAGCTCTGTGACCGCTGCGGACACGGCCGTGTATTACTGTGCGAGAGAGTATTACTATGATAGTAGTGGTTATTACTACGAATACTTCCAGCAGTGGGGCCAGGGCACCCTGGTCACCGTCTACTCAG", "CAGGTGCAGCTGCAGGAGTCGGGCCCAGGACTGGTGAAGCCTTCGGAGACCCTGTCCCTCACCTGCACTGTCTCTGGTGGCTCCGTCAGCAGTGGTAGTTACTACTGGAGCTGGATCAGGGAGCCCCCAGGGAAGGGACTGGAGTGGATTGGGTATATCTTTTACAGTGGGAGCACCAACTACAACCCCTCCCTCAAGAGTCGAGTCACCATATCAGTAGACACGTCCAAGAACCAGTTCTCCCTGAAGCTGAGCTCTGTGACCGCTGCGGACACGGCCGTGTATTACTGTGCGAGAGAGTATTACTATGATAGTAGTGGTTATTACTACGAATACTTCCAGCACTGGGGCCAGGGCACCCTGGTCACCGTCTCCTCAG", "AAGGTGCCGCTGCAGGAGTCGGGCCCAGGACTGGTGAAGCCTTCGGAGACCCTGTCCCTCACCTGCACTGTCTCTGGTGGTTCCGTCAACAGTGGTAGTTACTACTGGAGCTGGATCCGGCAGCCCCCAGGGAAGGGACTGGAGTGGATTGGGTATATCTATTACAGTGGGAGCACCAACTACAACCCCTCCCTCAAGAGTCGAGTCACCATATCAGTAGACACGTCCAAGAACCAGTTCTCCCTGAAGCTGAGCTCTGTGACCGCTGCGGACACGGCCGTGTATTACTGTGCGAGAGAGTATTACTATGATAGTAGTGGTTATTACTACGAATACTTCCAGCAGTGGGGCCAGGGCACCCTGGTCACCGTCTACTCAG", "CAGGTGCAACTGCAGGAGTCGGGCCCAGGACTGGTGAAGCCTTCGGAGACCCTGTCCCTCACCTGCACTGTCTCTGGTGGCTCCGTCAGCAGTGGTAGTTACTACTGGAGCTGGATCCGGCAGCCCCCAGGGAAGGGACTGGAGTGGATTGGGTATATCTATTACAGTGGGAGCACCAACTACAACCCCTCCCTCAAGAGTCGAGTCACCATATCAGTAGACACGTCCAAGAACCAGTTCTCCCTGAAGCTGAGCTCTGTGACCGCTGCGGACACGGCCGTGTATTACTGTGCGAGAGAGTATTACTATGATAGTAGTGGTTATTACTACAAATACTTCCAGCACTGGGGCCAGGGCACCCTGGTCATCGTCTCCTCAG", "CAGGTGCAGCTGCAGGAGTCGGGCCCAGGACTGGTGAAGCCTTCGGAGACCCTGTCCCTCACCTGCACTGTCTCTGGTGGCTCCGTCAGCAGTGGTAGTTACTACTGGAGCTGGATCCGGCAGCCCCCAGGGAAGGGACTGGAGTGGATTGGGTATATCTATTACAGTGGGAGCACCAACTACAACCCCTCCCTCAAGAGTCGAGTCACCATATCAGTAGACACGTCCAAGAACCAGTTCTCCCTGAAGCTGAGCTCTGTGACCGCTGCGGACACGGCCGTGTATTACTGTGCGAGAGAGTATTACTATGATAGTAGTGGTTATTACTACGAATACTTCCAGCACTGGGGCCAGGGCACCCTGGTAACCGTCTCCTCAG", "CAGGTGAAGCTGCAGGAGTCGGGCCCAGGACTGGTGAAGCCTTCGGAGACCCTGTCCCTCACCTGCACTGTCTCTGGTGGCTCCGTCAGCAGTGGTAGTTACTACTGGAGCTGGATCCGGCAGCCCCCAGGGAAGGGACTGGAGTGGATTGGGTATATCTATTACAGTGGGAGCACCAACTACAACCCCTCCCTCAAGAGTCGAGTCACCATATCAGTAGACACATCCAGGAACCAGTTCTCCCTGAAGCTGAGCTCTGTGACCGCTGCGGACACGGCCGTGTATTACTGTGCGAGAGAGTATTACTATGATAGTAGTGGTTATTACTACGAATACTTCCAGCATTGGGGCCAGGGCACCCTGGTCACCGTCTCCTCAG", "CAGGTGCAGCTGGTCTGAATGTGCAATGGTCCTAAACAGGAGTCGGGCCCAGCACTGGTGAAGCCTTCGGAGACCCTGTCCCTCACCTGCACTGTCTCTGGTGGCTCCGTCAGCAGTGGTAGTTACTACTGGAGCTGGATCCGGCAGCCCCCAGGGAAGGGACTGGAGTGGATTGGGTATATCTATTACAGTGGGAGCACCAACTACAACCCCTCCCTCAAGAGTCGAGTCACCATATCAGTAGACACGTCCAAGAACCAGTTCTCCCTGAAGCTGAGCTCTGTGACCGCTGCGGACACGGCCGTGTATTACTGTGCGAGAGAGTATTACTATGATAGTAGTGGTTATTACTACGAATACTTCCAGCACTGGCGCCAGGGCACCCTGGTCACCGTCTCCTCAG", "CAGGTGCAGCTGCAGGAATCGGGCCCAGGACTGGTGAAGCCTTCGGAGACCCTGTCCCTCACCTGCGCTGTCTCTGGTGGCTCCGTCAGCAGTGGTAGTTACTACTGGAGCTGGATCCGTCAGCCCCCAGGGAAGGGACTGGAGTGGATTGGGTATATCTATTACAGTGGGAGCACCAACTACAACCCCTCCCTCAAGAGTCGAGTCACCATATCAGTAGACACGTCCAAGAACCAGTTCTCCCTGAAGCTGAGCTCTGTGACCGCTGCGGACACGGCCGTGTATTACTGTGCGACAGAGTATTACTATGATAGTAGTGGTTATTACTACGAATACTTCCAGCACTGGGGCCAGGGCACCCTGGTCACCGTCTCCTCAG", "CAGGTGCAGCTGCAGGAGTCGGGCCCAGGACTGGTGAAGCCTTCGGAGACCCTGTCCCTCACCTGCACTGTCTCTGGTGGCTCCGTCAACAGTGGTAGTTACTCACTGGAGCTGGATCCGGCAGCCCCCAGGGAAGGGACTGGACTGGATTGGGTATATCTATTACAGTGGGAGCACCAACTACAACCCCTCCCTCAAGAGTCGAGTCACCATATCAGTAGACACGTCCAAGAACCAGTTCTTCCTGAAGCTGAGCTCTGTGACCGCTGCGGACACGGCCCTGTATTACTGTGCGAGAGAGTATCGCTATGGTAGTAGTGGTTATTACTACGAATACTTCCAGCACTGGGGCCAGGGCACCCTGGTCACCGTCTCCCCAG", "CAGATGCAGCTGCAGGAGTCGGGCCCAGGACTGGTGAAGCCTTCGGAGACTCTGTCCCTCACCTGCACTGTCTCTGGTGGCTGCGTCAGCAGTGGTAGTTACTACTGGAGCTGGACCCGGCAGCCCCCAGGGAAGGGACTGGAGTGGATTGGGTATATCTATTACAGTGGGAGCACCAACTACAACCCCTCCTTCAAGAGTCGAGTCACCATATCAGTGGACGCGTCCAAGAACCAGTTCTCCCTGAAGCTGAGCTCTGTGAGCGCTGCGGACACGGCCGTGTATTACTGTGCGAGAGAGTATTACTATGATAGTAGTGGTTATTACTACGAATACTTCCCGCACTGGGGCCAGGACACCCTGGTCACCGTCTCCTCAG", "CAGGTGCAGCTGCAGGAGTCGGGCCCAGGACTGGTGAAGCCTTCGGAGACCCTGTCCCTCACCTGCACTGTCTCTGGTGGCTCCGTCAGCAGTGGTAGTTACTACTGGAGCTGGATCCGGCAGCCCCCAGGGAAGGGACTGGAGTGGATTGGGTATATCTATTACAGTGGGAGCACCAACATACAACCCCTCCTTCAAGAGTCGAGTCACCATATCAGTAGACGCGTCCAAGAACCAGTTCTCCCTGAAGCTGAGCTCTGTGACCGCTGCGGACACGGCCGTGTATTACTGTGCGAGAGAGTATTACTATGATAGTAGTGGTTATTACTACGAATACTTCCAGCACTGGGGCCAGGACACCCTGGTCACCGTCTCCTCAG", "CAGGTGCAGCTGCAGGAGTCGGGCCCAGGACTGGTGAAGCCTTCGGAGACCCTGTCCCTCACCTGCACTGTCTCTGGTGGCTCCGTCAGCAGTGGTAGTTACTACTGGAGCTGGATCCGGCAGCCCCCAGGGAAGGGACTGGAGTGGATTGGGTATATCTATTACAGTGGGAGCACCAACTACAACCCCTCCTTCAAGAGTCGAGTCACCATATCAGTAGACGCGTCCAAGAACCAGTTCTCCCTGAAGCTGAGCTCTGTGACCGCTGCGGACACGGCCGTGTATTACTGTGCGAGAGAGTATTACTATGATAGTAGTGGTTATTACTACGAATACTTCCCGCACTGGGGCCAGGACACCCTGGTCACCGTCTCCTCAG", "CAAGTGCAGCTGCAGGAGTCGGGCCCAGGACTGGTGAAGCCTTCGGAGACCCTGTCCCTCACCTGCGCTGTCTCTGGTGGCTCCGTCAGCAGTGGTAGTTACTACTGGAGCTGGATCCGGCAGCCCCCAGGGAAGGGACTGGAGTGGATTGGGTATATCTATTACAGTGGGAGCACCAACTACAACCCCTCCCTCAAGAGTCGAGTCACCATATCAGTAGACACGTCCAAGAACCAGTTCTCCCTGAAGCTGAGCTCTGTGACCGCTGCGGACACGGCCGTGTATTACTGTACGAGAGAGTATTACTATGATAGTAGTGGTTATTACTACGAATACTTCCAGCACTGGGGCCAGGGCACCCTGGTCACCGTCTCCTCAG", "CAGGTGCAGCTGCAGGAGTCGGGCCCAGGACTGGTGAAGCCTTCGGAGACCCTGTCCCTCACCTGCACTGTCTCTGGTGGCTCCGTCAGCAGTGGTAGTTACTACTGGAGCTCGATCCGGCAGCCCCCAGGGAAGGGACTGGAGTGGATTGGGTATATCTATTACAGTGGGAGCACCAACTACAACCCCTCCTTCAAGAGTCGAGTCACCATATCAGTAGACGCGTCCAAGAACCAGTTCTCCCTGAAGCTGAGCTCTGTGACCGCTGCGGACACGGCCGTGTATTACTGTGCGAGAGAGTATTACTATGATAGTAGTGGTTATTACTACGAATACTTCCCGCACTGGGGCCAGGACACCCTGGTCACGGTCTCCTCAG"], "has_shm_indels": [false, true, false, true, false, false, false, false, false, false, false, false, false, false, true, false, true, false, true, false, false, false], "naive_seq": "CAGGTGCAGCTGCAGGAGTCGGGCCCAGGACTGGTGAAGCCTTCGGAGACCCTGTCCCTCACCTGCACTGTCTCTGGTGGCTCCGTCAGCAGTGGTAGTTACTACTGGAGCTGGATCCGGCAGCCCCCAGGGAAGGGACTGGAGTGGATTGGGTATATCTATTACAGTGGGAGCACCAACTACAACCCCTCCCTCAAGAGTCGAGTCACCATATCAGTAGACACGTCCAAGAACCAGTTCTCCCTGAAGCTGAGCTCTGTGACCGCTGCGGACACGGCCGTGTATTACTGTGCGAGAGAGTATTACTATGATAGTAGTGGTTATTACTACGAATACTTCCAGCACTGGGGCCAGGGCACCCTGGTCACCGTCTCCTCAG", "duplicates": [[], [], [], [], [], [], [], [], [], [], [], [], [], [], [], [], [], [], [], [], [], []], "v_3p_del": 0, "d_5p_del": 0, "d_3p_del": 0, "j_5p_del": 3, "v_5p_del": 0, "j_3p_del": 0, "vd_insertion": "", "dj_insertion": "", "fv_insertion": "", "jf_insertion": "", "mutated_invariants": [false, false, false, true, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false], "in_frames": [true, false, true, true, true, true, true, true, true, true, true, true, true, true, true, true, false, true, false, true, true, true], "stops": [false, true, false, false, false, false, false, false, false, false, false, false, false, false, true, false, true, false, true, false, false, false], "loci": ["igh", "igh", "igh", "igh", "igh", "igh", "igh", "igh", "igh", "igh", "igh", "igh", "igh", "igh", "igh", "igh", "igh", "igh", "igh", "igh", "igh", "igh"], "codon_positions": {"v": 288, "j": 345}}, {"qr_gap_seqs": ["", "", "GAGGTGCAGCTGCTGGAGTCTGGGGGAGGCTTGGTCCGGCCTGGGGGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGACTCACCGTCAGTAGCAACTACATGAGGTGGGTCCGCCAGGCTCTCAGGGAAGGGGCTGGAGTGGGTCTCAGTTAAAATTTATAGCGGTGGTAGCACATACTACGCAGACTCCGTGAAGGGCCGATTCACCATCTCCAGAGACAATTCCAAGAACACGCTGTATCTTCAAATGAACAGCCTGAGAGCTGAGGACACGGCTGTGTATTACTGTGCGAGAAGTATGATAACTGGTCTCAGAGACTACTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG", "", "", "", "GAGGTGCAGCTGCTGGAGTCTGGGCGGGAGGCTTGGTCCGGCCTGGGGGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGACTCACCGTCAGTAGCAACTACATGAGCTGGGTCCGCCAGGCTCCAGGGAAGGGGCTGGAGTGGGTCTCAGTTATTTATAGCGGTGGTAGCACATACTACGCAGACGGTCCGTGAAGGGCCGATTCACCATCTCCAGAGACAATTCCAAGAACACGCTGTATCTTCAAATAAACAGCCTGAGAGCTGAGGACACGGCTGTGTATTACTGTGCGAGAAGTATGATAACTGGTCTCAGAGACTACTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG", "", "", "", "", ""], "gl_gap_seqs": ["", "", "GAGGTGCAGCTGGTGGAGTCTGGGGGAGGCTTGGTCCAGCCTGGGGGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCGTCAGTAGCAACTACATGAGCTGGGTCCGCCAGGCTC.CAGGGAAGGGGCTGGAGTGGGTCTCAGTT...ATTTATAGCGGTGGTAGCACATACTACGCAGACTCCGTGAAGGGCCGATTCACCATCTCCAGAGACAATTCCAAGAACACGCTGTATCTTCAAATGAACAGCCTGAGAGCTGAGGACACGGCTGTGTATTACTGTGCGAGAAGTATGATAACTGGTCTCAGAGACTACTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG", "", "", "", "GAGGTGCAGCTGGTGGAGTCTGGG..GGAGGCTTGGTCCAGCCTGGGGGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCGTCAGTAGCAACTACATGAGCTGGGTCCGCCAGGCTCCAGGGAAGGGGCTGGAGTGGGTCTCAGTTATTTATAGCGGTGGTAGCACATACTACGCAGAC..TCCGTGAAGGGCCGATTCACCATCTCCAGAGACAATTCCAAGAACACGCTGTATCTTCAAATGAACAGCCTGAGAGCTGAGGACACGGCTGTGTATTACTGTGCGAGAAGTATGATAACTGGTCTCAGAGACTACTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG", "", "", "", "", ""], "indel_reversed_seqs": ["", "", "GAGGTGCAGCTGCTGGAGTCTGGGGGAGGCTTGGTCCGGCCTGGGGGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGACTCACCGTCAGTAGCAACTACATGAGGTGGGTCCGCCAGGCTCCAGGGAAGGGGCTGGAGTGGGTCTCAGTTATTTATAGCGGTGGTAGCACATACTACGCAGACTCCGTGAAGGGCCGATTCACCATCTCCAGAGACAATTCCAAGAACACGCTGTATCTTCAAATGAACAGCCTGAGAGCTGAGGACACGGCTGTGTATTACTGTGCGAGAAGTATGATAACTGGTCTCAGAGACTACTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG", "", "", "", "GAGGTGCAGCTGCTGGAGTCTGGGGGAGGCTTGGTCCGGCCTGGGGGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGACTCACCGTCAGTAGCAACTACATGAGCTGGGTCCGCCAGGCTCCAGGGAAGGGGCTGGAGTGGGTCTCAGTTATTTATAGCGGTGGTAGCACATACTACGCAGACTCCGTGAAGGGCCGATTCACCATCTCCAGAGACAATTCCAAGAACACGCTGTATCTTCAAATAAACAGCCTGAGAGCTGAGGACACGGCTGTGTATTACTGTGCGAGAAGTATGATAACTGGTCTCAGAGACTACTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG", "", "", "", "", ""], "reco_id": "a7dd2ff3bf", "tree": "[&R] ((((6b13522970:0.003958617453048627,(dd511fd81e:0.0011164015569204658,fdba07f2d2:0.0011164015569204658)bvz:0.0028422158961281608)ahz:0.0003011836820720619,((46e0a1c5ce:0.0004181377811213115,ae9764988c:0.0004181377811213115)tyz:0.003714495529278902,e2c05b0558:0.004132633310658557)fpq:0.00012716782456546885)osw:0.0005500323994163769,(((e86b47e3d3:0.0013932272233124544,ac52a46bb0:0.0013932272233124544)bqs:0.0016878677078929366,(cd9bc63afe:0.0026907932502602304,(6c21770612:0.0014407879914058854,d4ce68d359:0.0014407879914058854)ehq:0.0012500052579501428)ksu:0.0003903016805576458)bnz:0.0004043999183848849,7e5c759f54:0.003485494849202761)kpq:0.0013243386861093354)bin:0.0004999231562250227)glt:0.0;\n", "unique_ids": ["e2c05b0558", "fdba07f2d2", "e86b47e3d3", "7e5c759f54", "ae9764988c", "6b13522970", "d4ce68d359", "cd9bc63afe", "ac52a46bb0", "6c21770612", "dd511fd81e", "46e0a1c5ce"], "invalid": false, "v_gene": "IGHV3-66*02", "d_gene": "IGHD1-20*01", "j_gene": "IGHJ4*02", "cdr3_length": 39, "mut_freqs": [0.0, 0.0, 0.011363636363636364, 0.005681818181818182, 0.002840909090909091, 0.0, 0.011363636363636364, 0.008522727272727272, 0.011363636363636364, 0.008522727272727272, 0.0, 0.002840909090909091], "n_mutations": [0, 0, 4, 2, 1, 0, 4, 3, 4, 3, 0, 1], "input_seqs": ["GAGGTGCAGCTGGTGGAGTCTGGGGGAGGCTTGGTCCAGCCTGGGGGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCGTCAGTAGCAACTACATGAGCTGGGTCCGCCAGGCTCCAGGGAAGGGGCTGGAGTGGGTCTCAGTTATTTATAGCGGTGGTAGCACATACTACGCAGACTCCGTGAAGGGCCGATTCACCATCTCCAGAGACAATTCCAAGAACACGCTGTATCTTCAAATGAACAGCCTGAGAGCTGAGGACACGGCTGTGTATTACTGTGCGAGAAGTATGATAACTGGTCTCAGAGACTACTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG", "GAGGTGCAGCTGGTGGAGTCTGGGGGAGGCTTGGTCCAGCCTGGGGGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCGTCAGTAGCAACTACATGAGCTGGGTCCGCCAGGCTCCAGGGAAGGGGCTGGAGTGGGTCTCAGTTATTTATAGCGGTGGTAGCACATACTACGCAGACTCCGTGAAGGGCCGATTCACCATCTCCAGAGACAATTCCAAGAACACGCTGTATCTTCAAATGAACAGCCTGAGAGCTGAGGACACGGCTGTGTATTACTGTGCGAGAAGTATGATAACTGGTCTCAGAGACTACTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG", "GAGGTGCAGCTGCTGGAGTCTGGGGGAGGCTTGGTCCGGCCTGGGGGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGACTCACCGTCAGTAGCAACTACATGAGGTGGGTCCGCCAGGCTCTCAGGGAAGGGGCTGGAGTGGGTCTCAGTTAAAATTTATAGCGGTGGTAGCACATACTACGCAGACTCCGTGAAGGGCCGATTCACCATCTCCAGAGACAATTCCAAGAACACGCTGTATCTTCAAATGAACAGCCTGAGAGCTGAGGACACGGCTGTGTATTACTGTGCGAGAAGTATGATAACTGGTCTCAGAGACTACTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG", "GAGGTGCAGCTGCTGGAGTCTGGGGGAGGCTTGGTCCGGCCTGGGGGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCGTCAGTAGCAACTACATGAGCTGGGTCCGCCAGGCTCCAGGGAAGGGGCTGGAGTGGGTCTCAGTTATTTATAGCGGTGGTAGCACATACTACGCAGACTCCGTGAAGGGCCGATTCACCATCTCCAGAGACAATTCCAAGAACACGCTGTATCTTCAAATGAACAGCCTGAGAGCTGAGGACACGGCTGTGTATTACTGTGCGAGAAGTATGATAACTGGTCTCAGAGACTACTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG", "GAGGTGCAGCTGGTGGAGTCTGGGGGAGGCTTGGTCCAGCCTGGGGGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCGTCAGTAGCAACTACATGAGCTGGGTCCGCCAGGCTCCAGGGAAGGGGCTGGAGTGGCTCTCAGTTATTTATAGCGGTGGTAGCACATACTACGCAGACTCCGTGAAGGGCCGATTCACCATCTCCAGAGACAATTCCAAGAACACGCTGTATCTTCAAATGAACAGCCTGAGAGCTGAGGACACGGCTGTGTATTACTGTGCGAGAAGTATGATAACTGGTCTCAGAGACTACTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG", "GAGGTGCAGCTGGTGGAGTCTGGGGGAGGCTTGGTCCAGCCTGGGGGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCGTCAGTAGCAACTACATGAGCTGGGTCCGCCAGGCTCCAGGGAAGGGGCTGGAGTGGGTCTCAGTTATTTATAGCGGTGGTAGCACATACTACGCAGACTCCGTGAAGGGCCGATTCACCATCTCCAGAGACAATTCCAAGAACACGCTGTATCTTCAAATGAACAGCCTGAGAGCTGAGGACACGGCTGTGTATTACTGTGCGAGAAGTATGATAACTGGTCTCAGAGACTACTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG", "GAGGTGCAGCTGCTGGAGTCTGGGCGGGAGGCTTGGTCCGGCCTGGGGGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGACTCACCGTCAGTAGCAACTACATGAGCTGGGTCCGCCAGGCTCCAGGGAAGGGGCTGGAGTGGGTCTCAGTTATTTATAGCGGTGGTAGCACATACTACGCAGACGGTCCGTGAAGGGCCGATTCACCATCTCCAGAGACAATTCCAAGAACACGCTGTATCTTCAAATAAACAGCCTGAGAGCTGAGGACACGGCTGTGTATTACTGTGCGAGAAGTATGATAACTGGTCTCAGAGACTACTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG", "GAGGTGCAGCTGCTGGAGTCTGGGGGAGGCTTGGTCCGGCCTGGGGGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGACTCACCGTCAGTAGCAACTACATGAGCTGGGTCCGCCAGGCTCCAGGGAAGGGGCTGGAGTGGGTCTCAGTTATTTATAGCGGTGGTAGCACATACTACGCAGACTCCGTGAAGGGCCGATTCACCATCTCCAGAGACAATTCCAAGAACACGCTGTATCTTCAAATGAACAGCCTGAGAGCTGAGGACACGGCTGTGTATTACTGTGCGAGAAGTATGATAACTGGTCTCAGAGACTACTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG", "GAGGTGCAGCTGCTGGAGTCTGGGGGAGGCTTGGTCCGGCCTGGGGGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGACTCACCGTCAGTAGCAACTACATGAGGTGGGTCCGCCAGGCTCCAGGGAAGGGGCTGGAGTGGGTCTCAGTTATTTATAGCGGTGGTAGCACATACTACGCAGACTCCGTGAAGGGCCGATTCACCATCTCCAGAGACAATTCCAAGAACACGCTGTATCTTCAAATGAACAGCCTGAGAGCTGAGGACACGGCTGTGTATTACTGTGCGAGAAGTATGATAACTGGTCTCAGAGACTACTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG", "GAGGTGCAGCTGCTGGAGTCTGGGGGAGGCTTGGTCCGGCCTGGGGGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGACTCACCGTCAGTAGCAACTACATGAGCTGGGTCCGCCAGGCTCCAGGGAAGGGGCTGGAGTGGGTCTCAGTTATTTATAGCGGTGGTAGCACATACTACGCAGACTCCGTGAAGGGCCGATTCACCATCTCCAGAGACAATTCCAAGAACACGCTGTATCTTCAAATGAACAGCCTGAGAGCTGAGGACACGGCTGTGTATTACTGTGCGAGAAGTATGATAACTGGTCTCAGAGACTACTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG", "GAGGTGCAGCTGGTGGAGTCTGGGGGAGGCTTGGTCCAGCCTGGGGGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCGTCAGTAGCAACTACATGAGCTGGGTCCGCCAGGCTCCAGGGAAGGGGCTGGAGTGGGTCTCAGTTATTTATAGCGGTGGTAGCACATACTACGCAGACTCCGTGAAGGGCCGATTCACCATCTCCAGAGACAATTCCAAGAACACGCTGTATCTTCAAATGAACAGCCTGAGAGCTGAGGACACGGCTGTGTATTACTGTGCGAGAAGTATGATAACTGGTCTCAGAGACTACTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG", "GAGGTGCAGCTGGTGGAGTCTGGGGGAGGCTTGGTCCAGCCTGGGGGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCGTCAGTAGCAACTACATGAGCTGGGTCCGCCAGGCTCCAGGGAAGGGGCTGGAGTGGCTCTCAGTTATTTATAGCGGTGGTAGCACATACTACGCAGACTCCGTGAAGGGCCGATTCACCATCTCCAGAGACAATTCCAAGAACACGCTGTATCTTCAAATGAACAGCCTGAGAGCTGAGGACACGGCTGTGTATTACTGTGCGAGAAGTATGATAACTGGTCTCAGAGACTACTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG"], "has_shm_indels": [false, false, true, false, false, false, true, false, false, false, false, false], "naive_seq": "GAGGTGCAGCTGGTGGAGTCTGGGGGAGGCTTGGTCCAGCCTGGGGGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCGTCAGTAGCAACTACATGAGCTGGGTCCGCCAGGCTCCAGGGAAGGGGCTGGAGTGGGTCTCAGTTATTTATAGCGGTGGTAGCACATACTACGCAGACTCCGTGAAGGGCCGATTCACCATCTCCAGAGACAATTCCAAGAACACGCTGTATCTTCAAATGAACAGCCTGAGAGCTGAGGACACGGCTGTGTATTACTGTGCGAGAAGTATGATAACTGGTCTCAGAGACTACTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG", "duplicates": [[], [], [], [], [], [], [], [], [], [], [], []], "v_3p_del": 2, "d_5p_del": 3, "d_3p_del": 7, "j_5p_del": 8, "v_5p_del": 0, "j_3p_del": 0, "vd_insertion": "AGTATG", "dj_insertion": "GTCTCAGA", "fv_insertion": "", "jf_insertion": "", "mutated_invariants": [false, false, false, false, false, false, false, false, false, false, false, false], "in_frames": [true, true, false, true, true, true, false, true, true, true, true, true], "stops": [false, false, true, false, false, false, true, false, false, false, false, false], "loci": ["igh", "igh", "igh", "igh", "igh", "igh", "igh", "igh", "igh", "igh", "igh", "igh"], "codon_positions": {"v": 282, "j": 318}}, {"qr_gap_seqs": ["", "", ""], "gl_gap_seqs": ["", "", ""], "indel_reversed_seqs": ["", "", ""], "reco_id": "962999a75d", "tree": "[&R] (((f168b0ec8b:0.10883939719606024,501a887172:0.10883939719606024)bhk:0.05242081694081897,24845562e3:0.1612602141368792)dkw:0.013742097852244105)agk:0.0;\n", "unique_ids": ["24845562e3", "501a887172", "f168b0ec8b"], "invalid": false, "v_gene": "IGHV3-66*02", "d_gene": "IGHD6-13*01", "j_gene": "IGHJ4*02", "cdr3_length": 33, "mut_freqs": [0.1791907514450867, 0.17630057803468208, 0.1994219653179191], "n_mutations": [62, 61, 69], "input_seqs": ["GAGGTGCAGCTGGTCCAGTTTGATGTAGGCTTGGTCCCGCTTAGGGGGTCCCTATGGCTCTCCTATGGAGCATCTGGCTTCACCGTCAGTGGCCACTACATGAGCTGGGTCTGCCAGGCTCCATGCAGGCGCCTGGAATGGGTCTCAGTAATTTATAGAGGTGGTACCAGTTCCTACACAGACTCCTTGAAGGGCCGATTCATCATCTCCACTGACAATTCCGATAACACGCTGTATCTTCAGGTCGACGGCCTGAGAGCGCAAAACACGGCTATGTATTACTGTGCACGCTCCTTAGCAGTTACCCGCTACTGGAGCCAAGGAACCCTGATCACCGTCTCATCAG", "TAGGTGCAATTGGTGGAGCGTGACAGAGACTTGGTCCTGCCTTGGGGCTCCCTGAGCCTCTTTTGTCCAGCCTCTGGATTCGCCGTCAGTAGCAACTCCATGACCTGGGTCTGTTACGCTCCAGGGAACAGCCTCCAATGGATCTCAGTTATTTATAGCGGTGGTAACACATACTACGCAGACTCCATGAAGGGCCTGTTCGCCATCTCTAAAGACAATTTCAAGAACACGTTATATCTTCAAATTAACCGCGTCTGAGCTCAAGACACGGGTGTGTATTACTGTGCGCGATCTATAACAGTAGTCGGCTGTTGGGGCCAGGGAACCGTACTGACCGTCTCCTCTC", "GAGGCGCAGCTGGTGGAGTGTAGCGGAGGCTTGATCCAACCTCGCGGCTCCCTCAGCCTCTTTTGTGCAGACTCTGGGTTCACCGTCAATAGAAACTCCATGAGCTGGGTCTACTACGTTCTAGGCAACAGCCTGGGCTGAATCTCAGTCATTTATAGCGCCGGTAACACATACTACGCAGACTCCATGATGGACCTGTTCACCATCTCTGGAGACAATTTCAAGAACACGCTATATCTCCAAATGACCAACCTCAGAACTGCAGACACGGTTGTATATTACTGTGCGCGATCTATAATACCAGCCGCCTGGTGGGGCCGGAGACTCGTAGTGACCGTCTCCTCAC"], "has_shm_indels": [false, false, false], "naive_seq": "GAGGTGCAGCTGGTGGAGTCTGGGGGAGGCTTGGTCCAGCCTGGGGGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCGTCAGTAGCAACTACATGAGCTGGGTCCGCCAGGCTCCAGGGAAGGGGCTGGAGTGGGTCTCAGTTATTTATAGCGGTGGTAGCACATACTACGCAGACTCCGTGAAGGGCCGATTCACCATCTCCAGAGACAATTCCAAGAACACGCTGTATCTTCAAATGAACAGCCTGAGAGCTGAGGACACGGCTGTGTATTACTGTGCGAGATCTATAGCAGCAGCCGACTACTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG", "duplicates": [[], [], []], "v_3p_del": 2, "d_5p_del": 3, "d_3p_del": 6, "j_5p_del": 8, "v_5p_del": 0, "j_3p_del": 0, "vd_insertion": "TC", "dj_insertion": "C", "fv_insertion": "", "jf_insertion": "", "mutated_invariants": [false, false, false], "in_frames": [true, true, true], "stops": [false, true, true], "loci": ["igh", "igh", "igh"], "codon_positions": {"v": 282, "j": 312}}, {"qr_gap_seqs": ["", "", "", "", ""], "gl_gap_seqs": ["", "", "", "", ""], "indel_reversed_seqs": ["", "", "", "", ""], "reco_id": "91f77d882f", "tree": "[&R] (((((37921756cc:-0.0,01430d7987:-0.0)qwz:-0.0,7c463a8e7c:-0.0)bwx:-0.0,5ac6e92281:-0.0)qxy:-0.0,5798aae16b:-0.0)dir:-0.0)ios:0.0;\n", "unique_ids": ["5798aae16b", "01430d7987", "5ac6e92281", "7c463a8e7c", "37921756cc"], "invalid": false, "v_gene": "IGHV5-51*01", "d_gene": "IGHD6-19*01", "j_gene": "IGHJ4*02", "cdr3_length": 48, "mut_freqs": [0.0, 0.0, 0.0, 0.0, 0.0], "n_mutations": [0, 0, 0, 0, 0], "input_seqs": ["GAGGTGCAGCTGGTGCAGTCTGGAGCAGAGGTGAAAAAGCCCGGGGAGTCTCTGAAGATCTCCTGTAAGGGTTCTGGATACAGCTTTACCAGCTACTGGATCGGCTGGGTGCGCCAGATGCCCGGGAAAGGCCTGGAGTGGATGGGGATCATCTATCCTGGTGACTCTGATACCAGATACAGCCCGTCCTTCCAAGGCCAGGTCACCATCTCAGCCGACAAGTCCATCAGCACCGCCTACCTGCAGTGGAGCAGCCTGAAGGCCTCGGACACCGCCATGTATTACTGTGCGAGACTAGGGTATAGCAGTGGCTGGTACTCGTTTGACTACTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG", "GAGGTGCAGCTGGTGCAGTCTGGAGCAGAGGTGAAAAAGCCCGGGGAGTCTCTGAAGATCTCCTGTAAGGGTTCTGGATACAGCTTTACCAGCTACTGGATCGGCTGGGTGCGCCAGATGCCCGGGAAAGGCCTGGAGTGGATGGGGATCATCTATCCTGGTGACTCTGATACCAGATACAGCCCGTCCTTCCAAGGCCAGGTCACCATCTCAGCCGACAAGTCCATCAGCACCGCCTACCTGCAGTGGAGCAGCCTGAAGGCCTCGGACACCGCCATGTATTACTGTGCGAGACTAGGGTATAGCAGTGGCTGGTACTCGTTTGACTACTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG", "GAGGTGCAGCTGGTGCAGTCTGGAGCAGAGGTGAAAAAGCCCGGGGAGTCTCTGAAGATCTCCTGTAAGGGTTCTGGATACAGCTTTACCAGCTACTGGATCGGCTGGGTGCGCCAGATGCCCGGGAAAGGCCTGGAGTGGATGGGGATCATCTATCCTGGTGACTCTGATACCAGATACAGCCCGTCCTTCCAAGGCCAGGTCACCATCTCAGCCGACAAGTCCATCAGCACCGCCTACCTGCAGTGGAGCAGCCTGAAGGCCTCGGACACCGCCATGTATTACTGTGCGAGACTAGGGTATAGCAGTGGCTGGTACTCGTTTGACTACTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG", "GAGGTGCAGCTGGTGCAGTCTGGAGCAGAGGTGAAAAAGCCCGGGGAGTCTCTGAAGATCTCCTGTAAGGGTTCTGGATACAGCTTTACCAGCTACTGGATCGGCTGGGTGCGCCAGATGCCCGGGAAAGGCCTGGAGTGGATGGGGATCATCTATCCTGGTGACTCTGATACCAGATACAGCCCGTCCTTCCAAGGCCAGGTCACCATCTCAGCCGACAAGTCCATCAGCACCGCCTACCTGCAGTGGAGCAGCCTGAAGGCCTCGGACACCGCCATGTATTACTGTGCGAGACTAGGGTATAGCAGTGGCTGGTACTCGTTTGACTACTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG", "GAGGTGCAGCTGGTGCAGTCTGGAGCAGAGGTGAAAAAGCCCGGGGAGTCTCTGAAGATCTCCTGTAAGGGTTCTGGATACAGCTTTACCAGCTACTGGATCGGCTGGGTGCGCCAGATGCCCGGGAAAGGCCTGGAGTGGATGGGGATCATCTATCCTGGTGACTCTGATACCAGATACAGCCCGTCCTTCCAAGGCCAGGTCACCATCTCAGCCGACAAGTCCATCAGCACCGCCTACCTGCAGTGGAGCAGCCTGAAGGCCTCGGACACCGCCATGTATTACTGTGCGAGACTAGGGTATAGCAGTGGCTGGTACTCGTTTGACTACTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG"], "has_shm_indels": [false, false, false, false, false], "naive_seq": "GAGGTGCAGCTGGTGCAGTCTGGAGCAGAGGTGAAAAAGCCCGGGGAGTCTCTGAAGATCTCCTGTAAGGGTTCTGGATACAGCTTTACCAGCTACTGGATCGGCTGGGTGCGCCAGATGCCCGGGAAAGGCCTGGAGTGGATGGGGATCATCTATCCTGGTGACTCTGATACCAGATACAGCCCGTCCTTCCAAGGCCAGGTCACCATCTCAGCCGACAAGTCCATCAGCACCGCCTACCTGCAGTGGAGCAGCCTGAAGGCCTCGGACACCGCCATGTATTACTGTGCGAGACTAGGGTATAGCAGTGGCTGGTACTCGTTTGACTACTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG", "duplicates": [[], [], [], [], []], "v_3p_del": 1, "d_5p_del": 0, "d_3p_del": 0, "j_5p_del": 5, "v_5p_del": 0, "j_3p_del": 0, "vd_insertion": "TA", "dj_insertion": "TCG", "fv_insertion": "", "jf_insertion": "", "mutated_invariants": [false, false, false, false, false], "in_frames": [true, true, true, true, true], "stops": [false, false, false, false, false], "loci": ["igh", "igh", "igh", "igh", "igh"], "codon_positions": {"v": 285, "j": 330}}, {"qr_gap_seqs": ["", "", "", ""], "gl_gap_seqs": ["", "", "", ""], "indel_reversed_seqs": ["", "", "", ""], "reco_id": "256bc9b5ab", "tree": "[&R] ((deaadfc443:0.002423026712814409,(a646646bdb:0.002062947063632044,(748a35a278:0.0009422850860372843,84f52131d2:0.0009422850860372843)enw:0.00112066197759476)bsx:0.00036007964898895)eiv:0.0002271527233139978)efl:0.0;\n", "unique_ids": ["deaadfc443", "748a35a278", "a646646bdb", "84f52131d2"], "invalid": false, "v_gene": "IGHV3-66*02", "d_gene": "IGHD6-6*01", "j_gene": "IGHJ4*02", "cdr3_length": 57, "mut_freqs": [0.0, 0.002702702702702703, 0.0, 0.002702702702702703], "n_mutations": [0, 1, 0, 1], "input_seqs": ["GAGGTGCAGCTGGTGGAGTCTGGGGGAGGCTTGGTCCAGCCTGGGGGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCGTCAGTAGCAACTACATGAGCTGGGTCCGCCAGGCTCCAGGGAAGGGGCTGGAGTGGGTCTCAGTTATTTATAGCGGTGGTAGCACATACTACGCAGACTCCGTGAAGGGCCGATTCACCATCTCCAGAGACAATTCCAAGAACACGCTGTATCTTCAAATGAACAGCCTGAGAGCTGAGGACACGGCTGTGTATTACTGTGCGAGAGAGTTTTGTGTCGGCAGGAGTATAGCAGCAGGGCGCCCTGACTACTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG", "GAGGTGCAGCTGGTGGAGTCTGGGGGAGGCTTGGTCCAGCCTGGGGGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCGTCAGTAGCAACTACATGAGCTGGGTCCGCCAGGCTCCAGGGAAGGGGCTGGAGTGGGTCTCAGTTATTAATAGCGGTGGTAGCACATACTACGCAGACTCCGTGAAGGGCCGATTCACCATCTCCAGAGACAATTCCAAGAACACGCTGTATCTTCAAATGAACAGCCTGAGAGCTGAGGACACGGCTGTGTATTACTGTGCGAGAGAGTTTTGTGTCGGCAGGAGTATAGCAGCAGGGCGCCCTGACTACTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG", "GAGGTGCAGCTGGTGGAGTCTGGGGGAGGCTTGGTCCAGCCTGGGGGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCGTCAGTAGCAACTACATGAGCTGGGTCCGCCAGGCTCCAGGGAAGGGGCTGGAGTGGGTCTCAGTTATTTATAGCGGTGGTAGCACATACTACGCAGACTCCGTGAAGGGCCGATTCACCATCTCCAGAGACAATTCCAAGAACACGCTGTATCTTCAAATGAACAGCCTGAGAGCTGAGGACACGGCTGTGTATTACTGTGCGAGAGAGTTTTGTGTCGGCAGGAGTATAGCAGCAGGGCGCCCTGACTACTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG", "GAGGTGCAGCTGGTGGAGTCTGGGGGAGGCTTGGTCCAGCCTGGGGGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCGTCAGTAGCAACTACATGAGCTGGGTCCGCCAGGCTCCAGGGAAGGGGCTGGAGTGGGTCTCAGTTATTTACAGCGGTGGTAGCACATACTACGCAGACTCCGTGAAGGGCCGATTCACCATCTCCAGAGACAATTCCAAGAACACGCTGTATCTTCAAATGAACAGCCTGAGAGCTGAGGACACGGCTGTGTATTACTGTGCGAGAGAGTTTTGTGTCGGCAGGAGTATAGCAGCAGGGCGCCCTGACTACTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG"], "has_shm_indels": [false, false, false, false], "naive_seq": "GAGGTGCAGCTGGTGGAGTCTGGGGGAGGCTTGGTCCAGCCTGGGGGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCGTCAGTAGCAACTACATGAGCTGGGTCCGCCAGGCTCCAGGGAAGGGGCTGGAGTGGGTCTCAGTTATTTATAGCGGTGGTAGCACATACTACGCAGACTCCGTGAAGGGCCGATTCACCATCTCCAGAGACAATTCCAAGAACACGCTGTATCTTCAAATGAACAGCCTGAGAGCTGAGGACACGGCTGTGTATTACTGTGCGAGAGAGTTTTGTGTCGGCAGGAGTATAGCAGCAGGGCGCCCTGACTACTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG", "duplicates": [[], [], [], []], "v_3p_del": 0, "d_5p_del": 0, "d_3p_del": 6, "j_5p_del": 7, "v_5p_del": 0, "j_3p_del": 0, "vd_insertion": "GTTTTGTGTCGGCAG", "dj_insertion": "AGGGCGCCC", "fv_insertion": "", "jf_insertion": "", "mutated_invariants": [false, false, false, false], "in_frames": [true, true, true, true], "stops": [false, false, false, false], "loci": ["igh", "igh", "igh", "igh"], "codon_positions": {"v": 282, "j": 336}}]}
test/new-results/test.log CHANGED
@@ -67,7 +67,7 @@ hmm
67
67
  --simultaneous-true-clonal-seqs: grouping seqs according to true partition
68
68
  warning split apart 1 cluster that contained multiple cdr3 lengths (total clusters: 10 --> 11)
69
69
  cluster splits: 8 --> 7 1
70
- subcluster annotating 11 clusters with steps: (0.3s) (0.1s) plotting performance
70
+ subcluster annotating 11 clusters with steps: (0.4s) (0.1s) plotting performance
71
71
  warning skipped annotation performance evaluation on 1 queries with different true and inferred net shm indel lengths: d8761c689a
72
72
  (0.0 sec)
73
73
 
@@ -213,67 +213,67 @@ hmm
213
213
  writing hmms removed 6 genes from glfo (leaving v 15 d 19 j 7)
214
214
  (0.7 sec)
215
215
  total time: 4.9
216
- simulate partis simulate --dont-write-git-info --parameter-dir test/new-results/test/parameters/data --n-sim-events 10 --n-trees 10 --n-leaf-distribution geometric --n-leaves 5 --no-per-base-mutation --random-seed 1 --n-procs 10 --outfname test/new-results/test/simu.yaml --indel-frequency 0.2
216
+ simulate partis simulate --dont-write-git-info --parameter-dir test/new-results/test/parameters/data --n-sim-events 10 --n-trees 10 --n-leaf-distribution geometric --n-leaves 5 --input-simulation-treefname /home/runner/work/partis/partis/test/trees.nwk --no-per-base-mutation --random-seed 1 --n-procs 10 --outfname test/new-results/test/simu.yaml --indel-frequency 0.2
217
217
  simulating
218
218
  --> proc 0
219
219
  reco params: test/new-results/test/parameters/data/hmm shm params: test/new-results/test/parameters/data/hmm
220
220
  using bpp uniform mutation with path /home/runner/work/partis/partis/packages/bpp
221
- made 1 event with 3 seqs in 0.1s (0.0s of which was running bppseqgen)
222
- total time: 5.6
221
+ made 1 event with 6 seqs in 0.1s (0.1s of which was running bppseqgen)
222
+ total time: 0.3
223
223
 
224
224
  --> proc 1
225
225
  reco params: test/new-results/test/parameters/data/hmm shm params: test/new-results/test/parameters/data/hmm
226
226
  using bpp uniform mutation with path /home/runner/work/partis/partis/packages/bpp
227
- made 1 event with 9 seqs in 0.1s (0.0s of which was running bppseqgen)
228
- total time: 5.8
227
+ made 1 event with 5 seqs in 0.1s (0.1s of which was running bppseqgen)
228
+ total time: 0.3
229
229
 
230
230
  --> proc 2
231
231
  reco params: test/new-results/test/parameters/data/hmm shm params: test/new-results/test/parameters/data/hmm
232
232
  using bpp uniform mutation with path /home/runner/work/partis/partis/packages/bpp
233
- made 1 event with 1 seqs in 0.1s (0.0s of which was running bppseqgen)
234
- total time: 5.9
233
+ made 1 event with 2 seqs in 0.2s (0.1s of which was running bppseqgen)
234
+ total time: 0.3
235
235
 
236
236
  --> proc 3
237
237
  reco params: test/new-results/test/parameters/data/hmm shm params: test/new-results/test/parameters/data/hmm
238
238
  using bpp uniform mutation with path /home/runner/work/partis/partis/packages/bpp
239
- made 1 event with 7 seqs in 0.2s (0.0s of which was running bppseqgen)
240
- total time: 5.7
239
+ made 1 event with 11 seqs in 0.2s (0.1s of which was running bppseqgen)
240
+ total time: 0.3
241
241
 
242
242
  --> proc 4
243
243
  reco params: test/new-results/test/parameters/data/hmm shm params: test/new-results/test/parameters/data/hmm
244
244
  using bpp uniform mutation with path /home/runner/work/partis/partis/packages/bpp
245
- made 1 event with 2 seqs in 0.1s (0.0s of which was running bppseqgen)
246
- total time: 6.0
245
+ made 1 event with 4 seqs in 0.1s (0.1s of which was running bppseqgen)
246
+ total time: 0.3
247
247
 
248
248
  --> proc 5
249
249
  reco params: test/new-results/test/parameters/data/hmm shm params: test/new-results/test/parameters/data/hmm
250
250
  using bpp uniform mutation with path /home/runner/work/partis/partis/packages/bpp
251
- made 1 event with 8 seqs in 0.2s (0.1s of which was running bppseqgen)
252
- total time: 5.9
251
+ made 1 event with 22 seqs in 0.3s (0.2s of which was running bppseqgen)
252
+ total time: 0.4
253
253
 
254
254
  --> proc 6
255
255
  reco params: test/new-results/test/parameters/data/hmm shm params: test/new-results/test/parameters/data/hmm
256
256
  using bpp uniform mutation with path /home/runner/work/partis/partis/packages/bpp
257
- made 1 event with 2 seqs in 0.1s (0.0s of which was running bppseqgen)
258
- total time: 5.9
257
+ made 1 event with 12 seqs in 0.2s (0.1s of which was running bppseqgen)
258
+ total time: 0.3
259
259
 
260
260
  --> proc 7
261
261
  reco params: test/new-results/test/parameters/data/hmm shm params: test/new-results/test/parameters/data/hmm
262
262
  using bpp uniform mutation with path /home/runner/work/partis/partis/packages/bpp
263
- made 1 event with 2 seqs in 0.1s (0.0s of which was running bppseqgen)
264
- total time: 5.8
263
+ made 1 event with 3 seqs in 0.1s (0.1s of which was running bppseqgen)
264
+ total time: 0.2
265
265
 
266
266
  --> proc 8
267
267
  reco params: test/new-results/test/parameters/data/hmm shm params: test/new-results/test/parameters/data/hmm
268
268
  using bpp uniform mutation with path /home/runner/work/partis/partis/packages/bpp
269
- made 1 event with 1 seqs in 0.1s (0.0s of which was running bppseqgen)
270
- total time: 5.4
269
+ made 1 event with 5 seqs in 0.2s (0.1s of which was running bppseqgen)
270
+ total time: 0.3
271
271
 
272
272
  --> proc 9
273
273
  reco params: test/new-results/test/parameters/data/hmm shm params: test/new-results/test/parameters/data/hmm
274
274
  using bpp uniform mutation with path /home/runner/work/partis/partis/packages/bpp
275
- made 1 event with 1 seqs in 0.1s (0.1s of which was running bppseqgen)
276
- total time: 5.7
275
+ made 1 event with 4 seqs in 0.2s (0.1s of which was running bppseqgen)
276
+ total time: 0.3
277
277
 
278
- read 10 events with 36 seqs from 10 .yaml files
279
- total time: 11.4
278
+ read 10 events with 74 seqs from 10 .yaml files
279
+ total time: 5.9
test/paired/new-results/partition-new-simu/fasttree/iclust-0/log CHANGED
@@ -16,8 +16,8 @@ Switched to using 20 rate categories (CAT approximation)
16
16
  Rate categories were divided by 0.666 so that average rate = 1.0
17
17
  CAT-based log-likelihoods may not be comparable across runs
18
18
  Use -gamma for approximate but comparable Gamma(20) log-likelihoods
19
- ML-NNI round 2: LogLk = -1661.140 NNIs 0 max delta 0.00 Time 0.06
19
+ ML-NNI round 2: LogLk = -1661.140 NNIs 0 max delta 0.00 Time 0.07
20
20
  Turning off heuristics for final round of ML NNIs (converged)
21
21
  ML-NNI round 3: LogLk = -1661.140 NNIs 0 max delta 0.00 Time 0.08 (final)
22
- Optimize all lengths: LogLk = -1661.140 Time 0.08
22
+ Optimize all lengths: LogLk = -1661.140 Time 0.09
23
23
  Total time: 0.10 seconds Unique: 8/8 Bad splits: 0/5
test/paired/new-results/partition-new-simu/fasttree/iclust-1/log CHANGED
@@ -16,8 +16,8 @@ Switched to using 20 rate categories (CAT approximation)
16
16
  Rate categories were divided by 0.652 so that average rate = 1.0
17
17
  CAT-based log-likelihoods may not be comparable across runs
18
18
  Use -gamma for approximate but comparable Gamma(20) log-likelihoods
19
- ML-NNI round 2: LogLk = -1478.013 NNIs 0 max delta 0.00 Time 0.06
19
+ ML-NNI round 2: LogLk = -1478.013 NNIs 0 max delta 0.00 Time 0.07
20
20
  Turning off heuristics for final round of ML NNIs (converged)
21
- ML-NNI round 3: LogLk = -1478.012 NNIs 0 max delta 0.00 Time 0.07 (final)
22
- Optimize all lengths: LogLk = -1478.012 Time 0.07
23
- Total time: 0.08 seconds Unique: 8/8 Bad splits: 0/5
21
+ ML-NNI round 3: LogLk = -1478.012 NNIs 0 max delta 0.00 Time 0.09 (final)
22
+ Optimize all lengths: LogLk = -1478.012 Time 0.09
23
+ Total time: 0.10 seconds Unique: 8/8 Bad splits: 0/5
test/paired/new-results/partition-new-simu/fasttree/iclust-2/log CHANGED
@@ -16,8 +16,8 @@ Switched to using 20 rate categories (CAT approximation)
16
16
  Rate categories were divided by 0.641 so that average rate = 1.0
17
17
  CAT-based log-likelihoods may not be comparable across runs
18
18
  Use -gamma for approximate but comparable Gamma(20) log-likelihoods
19
- ML-NNI round 2: LogLk = -1274.921 NNIs 0 max delta 0.00 Time 0.05
19
+ ML-NNI round 2: LogLk = -1274.921 NNIs 0 max delta 0.00 Time 0.04
20
20
  Turning off heuristics for final round of ML NNIs (converged)
21
- ML-NNI round 3: LogLk = -1274.921 NNIs 0 max delta 0.00 Time 0.06 (final)
22
- Optimize all lengths: LogLk = -1274.921 Time 0.07
23
- Total time: 0.07 seconds Unique: 6/6 Bad splits: 0/3
21
+ ML-NNI round 3: LogLk = -1274.921 NNIs 0 max delta 0.00 Time 0.04 (final)
22
+ Optimize all lengths: LogLk = -1274.921 Time 0.05
23
+ Total time: 0.05 seconds Unique: 6/6 Bad splits: 0/3