@jbrowse/plugin-variants 2.5.0 → 2.6.2

package/src/VariantTrack/configSchema.ts

@@ -1,24 +0,0 @@
-import { ConfigurationSchema } from '@jbrowse/core/configuration'
-import { createBaseTrackConfig } from '@jbrowse/core/pluggableElementTypes'
-import PluginManager from '@jbrowse/core/PluginManager'
-
-/**
- * #config VariantTrack
- * Mostly similar to feature track, but has `ChordDisplayType` registered to it,
- * and custom feature details in `LinearVariantDisplay`
- */
-function x() {} // eslint-disable-line @typescript-eslint/no-unused-vars
-
-const configSchema = (pluginManager: PluginManager) =>
-  ConfigurationSchema(
-    'VariantTrack',
-    {},
-    {
-      /**
-       * #baseConfiguration
-       */
-      baseConfiguration: createBaseTrackConfig(pluginManager),
-    },
-  )
-
-export default configSchema

package/src/VariantTrack/index.ts

@@ -1,16 +0,0 @@
-import PluginManager from '@jbrowse/core/PluginManager'
-import TrackType from '@jbrowse/core/pluggableElementTypes/TrackType'
-import { createBaseTrackModel } from '@jbrowse/core/pluggableElementTypes/models'
-import configSchemaF from './configSchema'
-
-export default (pm: PluginManager) => {
-  pm.addTrackType(() => {
-    const configSchema = configSchemaF(pm)
-    return new TrackType({
-      name: 'VariantTrack',
-      displayName: 'Variant track',
-      configSchema,
-      stateModel: createBaseTrackModel(pm, 'VariantTrack', configSchema),
-    })
-  })
-}

package/src/VcfAdapter/VcfAdapter.test.ts

@@ -1,28 +0,0 @@
-import { toArray } from 'rxjs/operators'
-import { firstValueFrom } from 'rxjs'
-import Adapter from './VcfAdapter'
-import configSchema from './configSchema'
-
-test('adapter can fetch variants from volvox.vcf', async () => {
-  const adapter = new Adapter(
-    configSchema.create({
-      vcfLocation: {
-        localPath: require.resolve('./test_data/volvox.filtered.vcf'),
-        locationType: 'LocalPathLocation',
-      },
-    }),
-  )
-
-  const feat = adapter.getFeatures({
-    assemblyName: 'volvox',
-    refName: 'ctgA',
-    start: 0,
-    end: 20000,
-  })
-
-  const names = await adapter.getRefNames()
-  expect(names).toMatchSnapshot()
-
-  const featArray = await firstValueFrom(feat.pipe(toArray()))
-  expect(featArray.slice(0, 5)).toMatchSnapshot()
-})

package/src/VcfAdapter/VcfAdapter.ts

@@ -1,125 +0,0 @@
-import {
-  BaseFeatureDataAdapter,
-  BaseOptions,
-} from '@jbrowse/core/data_adapters/BaseAdapter'
-import { Region, Feature } from '@jbrowse/core/util'
-import { openLocation } from '@jbrowse/core/util/io'
-import { ObservableCreate } from '@jbrowse/core/util/rxjs'
-import IntervalTree from '@flatten-js/interval-tree'
-import { unzip } from '@gmod/bgzf-filehandle'
-import VCF from '@gmod/vcf'
-
-// local
-import VcfFeature from '../VcfFeature'
-
-const readVcf = (f: string) => {
-  const header: string[] = []
-  const rest: string[] = []
-  f.split(/\n|\r\n|\r/)
-    .map(f => f.trim())
-    .filter(f => !!f)
-    .forEach(line => {
-      if (line.startsWith('#')) {
-        header.push(line)
-      } else if (line) {
-        rest.push(line)
-      }
-    })
-  return { header: header.join('\n'), lines: rest }
-}
-
-function isGzip(buf: Buffer) {
-  return buf[0] === 31 && buf[1] === 139 && buf[2] === 8
-}
-
-export default class VcfAdapter extends BaseFeatureDataAdapter {
-  public static capabilities = ['getFeatures', 'getRefNames']
-
-  protected vcfFeatures?: Promise<{
-    header: string
-    intervalTree: Record<string, IntervalTree>
-  }>
-
-  public async getHeader() {
-    const { header } = await this.setup()
-    return header
-  }
-
-  async getMetadata() {
-    const { header } = await this.setup()
-    const parser = new VCF({ header: header })
-    return parser.getMetadata()
-  }
-
-  // converts lines into an interval tree
-  public async setupP() {
-    const pm = this.pluginManager
-    const buf = await openLocation(this.getConf('vcfLocation'), pm).readFile()
-
-    const buffer = isGzip(buf) ? await unzip(buf) : buf
-
-    // 512MB  max chrome string length is 512MB
-    if (buffer.length > 536_870_888) {
-      throw new Error('Data exceeds maximum string length (512MB)')
-    }
-
-    const str = new TextDecoder().decode(buffer)
-    const { header, lines } = readVcf(str)
-    const intervalTree = {} as { [key: string]: IntervalTree }
-
-    for (const obj of lines.map((line, id) => {
-      const [refName, startP, , ref, , , , info] = line.split('\t')
-      const start = +startP - 1
-      const def = start + ref.length
-      const end = +(info.match(/END=(\d+)/)?.[1].trim() || def)
-      return { line, refName, start, end, id }
-    })) {
-      const key = obj.refName
-      if (!intervalTree[key]) {
-        intervalTree[key] = new IntervalTree()
-      }
-      intervalTree[key].insert([obj.start, obj.end], obj)
-    }
-
-    return { header, intervalTree }
-  }
-
-  public async setup() {
-    if (!this.vcfFeatures) {
-      this.vcfFeatures = this.setupP().catch(e => {
-        this.vcfFeatures = undefined
-        throw e
-      })
-    }
-    return this.vcfFeatures
-  }
-
-  public async getRefNames(_: BaseOptions = {}) {
-    const { intervalTree } = await this.setup()
-    return Object.keys(intervalTree)
-  }
-
-  public getFeatures(region: Region, opts: BaseOptions = {}) {
-    return ObservableCreate<Feature>(async observer => {
-      try {
-        const { start, end, refName } = region
-        const { header, intervalTree } = await this.setup()
-        const parser = new VCF({ header })
-        intervalTree[refName]?.search([start, end]).forEach(f =>
-          observer.next(
-            new VcfFeature({
-              variant: parser.parseLine(f.line),
-              parser,
-              id: `${this.id}-${f.id}`,
-            }),
-          ),
-        )
-        observer.complete()
-      } catch (e) {
-        observer.error(e)
-      }
-    }, opts.signal)
-  }
-
-  public freeResources(): void {}
-}

package/src/VcfAdapter/__snapshots__/VcfAdapter.test.ts.snap

@@ -1,325 +0,0 @@
-// Jest Snapshot v1, https://goo.gl/fbAQLP
-
-exports[`adapter can fetch variants from volvox.vcf 1`] = `
-[
-  "ctgA",
-]
-`;
-
-exports[`adapter can fetch variants from volvox.vcf 2`] = `
-[
-  {
-    "ALT": [
-      "C",
-    ],
-    "CHROM": "ctgA",
-    "FILTER": null,
-    "ID": null,
-    "INFO": {
-      "AC1": [
-        2,
-      ],
-      "AF1": [
-        1,
-      ],
-      "DP": [
-        3,
-      ],
-      "DP4": [
-        0,
-        0,
-        3,
-        0,
-      ],
-      "FQ": [
-        -36,
-      ],
-      "MQ": [
-        37,
-      ],
-      "VDB": [
-        0.0186,
-      ],
-    },
-    "POS": 277,
-    "QUAL": 10.4,
-    "REF": "T",
-    "aliases": undefined,
-    "description": "SNV T -> C",
-    "end": 277,
-    "name": undefined,
-    "refName": "ctgA",
-    "samples": {
-      "sample_data/raw/volvox/volvox-sorted.bam": {
-        "GQ": [
-          13,
-        ],
-        "GT": [
-          "1/1",
-        ],
-        "PL": [
-          42,
-          9,
-          0,
-        ],
-      },
-    },
-    "start": 276,
-    "type": "SNV",
-    "uniqueId": "test-0",
-  },
-  {
-    "ALT": [
-      "C",
-    ],
-    "CHROM": "ctgA",
-    "FILTER": null,
-    "ID": null,
-    "INFO": {
-      "AC1": [
-        2,
-      ],
-      "AF1": [
-        1,
-      ],
-      "DP": [
-        23,
-      ],
-      "DP4": [
-        0,
-        1,
-        8,
-        14,
-      ],
-      "FQ": [
-        -73,
-      ],
-      "MQ": [
-        37,
-      ],
-      "PV4": [
-        1,
-        1,
-        0.42,
-        1,
-      ],
-      "VDB": [
-        0.0308,
-      ],
-    },
-    "POS": 1694,
-    "QUAL": 107,
-    "REF": "T",
-    "aliases": undefined,
-    "description": "SNV T -> C",
-    "end": 1694,
-    "name": undefined,
-    "refName": "ctgA",
-    "samples": {
-      "sample_data/raw/volvox/volvox-sorted.bam": {
-        "GQ": [
-          89,
-        ],
-        "GT": [
-          "1/1",
-        ],
-        "PL": [
-          140,
-          46,
-          0,
-        ],
-      },
-    },
-    "start": 1693,
-    "type": "SNV",
-    "uniqueId": "test-1",
-  },
-  {
-    "ALT": [
-      "G",
-    ],
-    "CHROM": "ctgA",
-    "FILTER": null,
-    "ID": null,
-    "INFO": {
-      "AC1": [
-        1,
-      ],
-      "AF1": [
-        0.5,
-      ],
-      "DP": [
-        22,
-      ],
-      "DP4": [
-        6,
-        5,
-        3,
-        8,
-      ],
-      "FQ": [
-        45.3,
-      ],
-      "MQ": [
-        37,
-      ],
-      "PV4": [
-        0.39,
-        1,
-        1,
-        1,
-      ],
-      "VDB": [
-        0.0253,
-      ],
-    },
-    "POS": 2644,
-    "QUAL": 44,
-    "REF": "T",
-    "aliases": undefined,
-    "description": "SNV T -> G",
-    "end": 2644,
-    "name": undefined,
-    "refName": "ctgA",
-    "samples": {
-      "sample_data/raw/volvox/volvox-sorted.bam": {
-        "GQ": [
-          75,
-        ],
-        "GT": [
-          "0/1",
-        ],
-        "PL": [
-          74,
-          0,
-          77,
-        ],
-      },
-    },
-    "start": 2643,
-    "type": "SNV",
-    "uniqueId": "test-2",
-  },
-  {
-    "ALT": [
-      "A",
-    ],
-    "CHROM": "ctgA",
-    "FILTER": null,
-    "ID": null,
-    "INFO": {
-      "AC1": [
-        2,
-      ],
-      "AF1": [
-        1,
-      ],
-      "DP": [
-        19,
-      ],
-      "DP4": [
-        0,
-        0,
-        8,
-        11,
-      ],
-      "FQ": [
-        -84,
-      ],
-      "MQ": [
-        36,
-      ],
-      "VDB": [
-        0.0384,
-      ],
-    },
-    "POS": 3213,
-    "QUAL": 124,
-    "REF": "T",
-    "aliases": undefined,
-    "description": "SNV T -> A",
-    "end": 3213,
-    "name": undefined,
-    "refName": "ctgA",
-    "samples": {
-      "sample_data/raw/volvox/volvox-sorted.bam": {
-        "GQ": [
-          99,
-        ],
-        "GT": [
-          "1/1",
-        ],
-        "PL": [
-          157,
-          57,
-          0,
-        ],
-      },
-    },
-    "start": 3212,
-    "type": "SNV",
-    "uniqueId": "test-3",
-  },
-  {
-    "ALT": [
-      "ct",
-    ],
-    "CHROM": "ctgA",
-    "FILTER": null,
-    "ID": null,
-    "INFO": {
-      "AC1": [
-        2,
-      ],
-      "AF1": [
-        1,
-      ],
-      "DP": [
-        15,
-      ],
-      "DP4": [
-        0,
-        0,
-        5,
-        6,
-      ],
-      "FQ": [
-        -67.5,
-      ],
-      "INDEL": true,
-      "MQ": [
-        37,
-      ],
-      "VDB": [
-        0.0384,
-      ],
-    },
-    "POS": 3858,
-    "QUAL": 160,
-    "REF": "ctt",
-    "aliases": undefined,
-    "description": "deletion ctt -> ct",
-    "end": 3860,
-    "name": undefined,
-    "refName": "ctgA",
-    "samples": {
-      "sample_data/raw/volvox/volvox-sorted.bam": {
-        "GQ": [
-          63,
-        ],
-        "GT": [
-          "1/1",
-        ],
-        "PL": [
-          201,
-          33,
-          0,
-        ],
-      },
-    },
-    "start": 3857,
-    "type": "deletion",
-    "uniqueId": "test-4",
-  },
-]
-`;

package/src/VcfAdapter/configSchema.ts

@@ -1,22 +0,0 @@
-import { ConfigurationSchema } from '@jbrowse/core/configuration'
-
-/**
- * #config VcfAdapter
- */
-function x() {} // eslint-disable-line @typescript-eslint/no-unused-vars
-
-const VcfAdapter = ConfigurationSchema(
-  'VcfAdapter',
-  {
-    /**
-     * #slot
-     */
-    vcfLocation: {
-      type: 'fileLocation',
-      defaultValue: { uri: '/path/to/my.vcf', locationType: 'UriLocation' },
-    },
-  },
-  { explicitlyTyped: true },
-)
-
-export default VcfAdapter

package/src/VcfAdapter/index.ts

@@ -1,15 +0,0 @@
-import PluginManager from '@jbrowse/core/PluginManager'
-import AdapterType from '@jbrowse/core/pluggableElementTypes/AdapterType'
-import configSchema from './configSchema'
-
-export default (pluginManager: PluginManager) => {
-  pluginManager.addAdapterType(
-    () =>
-      new AdapterType({
-        name: 'VcfAdapter',
-        displayName: 'VCF adapter',
-        configSchema,
-        getAdapterClass: () => import('./VcfAdapter').then(r => r.default),
-      }),
-  )
-}

package/src/VcfAdapter/test_data/volvox.filtered.vcf

@@ -1,73 +0,0 @@
-##fileformat=VCFv4.1
-##samtoolsVersion=0.1.18 (r982:295)
-##INFO=<ID=DP,Number=1,Type=Integer,Description="Raw read depth">
-##INFO=<ID=DP4,Number=4,Type=Integer,Description="# high-quality ref-forward bases, ref-reverse, alt-forward and alt-reverse bases">
-##INFO=<ID=MQ,Number=1,Type=Integer,Description="Root-mean-square mapping quality of covering reads">
-##INFO=<ID=FQ,Number=1,Type=Float,Description="Phred probability of all samples being the same">
-##INFO=<ID=AF1,Number=1,Type=Float,Description="Max-likelihood estimate of the first ALT allele frequency (assuming HWE)">
-##INFO=<ID=AC1,Number=1,Type=Float,Description="Max-likelihood estimate of the first ALT allele count (no HWE assumption)">
-##INFO=<ID=G3,Number=3,Type=Float,Description="ML estimate of genotype frequencies">
-##INFO=<ID=HWE,Number=1,Type=Float,Description="Chi^2 based HWE test P-value based on G3">
-##INFO=<ID=CLR,Number=1,Type=Integer,Description="Log ratio of genotype likelihoods with and without the constraint">
-##INFO=<ID=UGT,Number=1,Type=String,Description="The most probable unconstrained genotype configuration in the trio">
-##INFO=<ID=CGT,Number=1,Type=String,Description="The most probable constrained genotype configuration in the trio">
-##INFO=<ID=PV4,Number=4,Type=Float,Description="P-values for strand bias, baseQ bias, mapQ bias and tail distance bias">
-##INFO=<ID=INDEL,Number=0,Type=Flag,Description="Indicates that the variant is an INDEL.">
-##INFO=<ID=PC2,Number=2,Type=Integer,Description="Phred probability of the nonRef allele frequency in group1 samples being larger (,smaller) than in group2.">
-##INFO=<ID=PCHI2,Number=1,Type=Float,Description="Posterior weighted chi^2 P-value for testing the association between group1 and group2 samples.">
-##INFO=<ID=QCHI2,Number=1,Type=Integer,Description="Phred scaled PCHI2.">
-##INFO=<ID=PR,Number=1,Type=Integer,Description="# permutations yielding a smaller PCHI2.">
-##INFO=<ID=VDB,Number=1,Type=Float,Description="Variant Distance Bias">
-##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
-##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Genotype Quality">
-##FORMAT=<ID=GL,Number=3,Type=Float,Description="Likelihoods for RR,RA,AA genotypes (R=ref,A=alt)">
-##FORMAT=<ID=DP,Number=1,Type=Integer,Description="# high-quality bases">
-##FORMAT=<ID=SP,Number=1,Type=Integer,Description="Phred-scaled strand bias P-value">
-##FORMAT=<ID=PL,Number=G,Type=Integer,Description="List of Phred-scaled genotype likelihoods">
-##contig=<ID=ctgA,length=248956422,assembly=GRCh38.d1.vd1>
-#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	sample_data/raw/volvox/volvox-sorted.bam
-ctgA	277	.	T	C	10.4	.	DP=3;VDB=0.0186;AF1=1;AC1=2;DP4=0,0,3,0;MQ=37;FQ=-36	GT:PL:GQ	1/1:42,9,0:13
-ctgA	1694	.	T	C	107	.	DP=23;VDB=0.0308;AF1=1;AC1=2;DP4=0,1,8,14;MQ=37;FQ=-73;PV4=1,1,0.42,1	GT:PL:GQ	1/1:140,46,0:89
-ctgA	2644	.	T	G	44	.	DP=22;VDB=0.0253;AF1=0.5;AC1=1;DP4=6,5,3,8;MQ=37;FQ=45.3;PV4=0.39,1,1,1	GT:PL:GQ	0/1:74,0,77:75
-ctgA	3213	.	T	A	124	.	DP=19;VDB=0.0384;AF1=1;AC1=2;DP4=0,0,8,11;MQ=36;FQ=-84	GT:PL:GQ	1/1:157,57,0:99
-ctgA	3858	.	ctt	ct	160	.	INDEL;DP=15;VDB=0.0384;AF1=1;AC1=2;DP4=0,0,5,6;MQ=37;FQ=-67.5	GT:PL:GQ	1/1:201,33,0:63
-ctgA	5496	.	C	G	6.98	.	DP=18;VDB=0.0011;AF1=0.4999;AC1=1;DP4=5,7,4,2;MQ=37;FQ=9.53;PV4=0.62,1,1,1	GT:PL:GQ	0/1:36,0,92:37
-ctgA	8471	.	G	T	124	.	DP=21;VDB=0.0355;AF1=1;AC1=2;DP4=0,0,11,10;MQ=37;FQ=-90	GT:PL:GQ	1/1:157,63,0:99
-ctgA	9603	.	A	T	126	.	DP=21;VDB=0.0356;AF1=1;AC1=2;DP4=0,0,10,11;MQ=36;FQ=-90	GT:PL:GQ	1/1:159,63,0:99
-ctgA	10423	.	T	A	25	.	DP=19;VDB=0.0404;AF1=0.5;AC1=1;DP4=3,7,3,6;MQ=37;FQ=28;PV4=1,1,1,0.27	GT:PL:GQ	0/1:55,0,73:58
-ctgA	13202	.	G	T	40	.	DP=22;VDB=0.0399;AF1=0.5;AC1=1;DP4=4,8,5,5;MQ=37;FQ=42.8;PV4=0.67,1,1,1	GT:PL:GQ	0/1:70,0,84:73
-ctgA	14247	.	ac	aCc	61.5	.	INDEL;DP=22;VDB=0.0404;AF1=0.5;AC1=1;DP4=3,4,6,0;MQ=37;FQ=62.4;PV4=0.07,1,1,1	GT:PL:GQ	0/1:99,0,101:99
-ctgA	14481	.	G	A	42	.	DP=21;VDB=0.0394;AF1=0.5;AC1=1;DP4=4,6,5,6;MQ=37;FQ=42;PV4=1,1,1,0.12	GT:PL:GQ	0/1:72,0,72:72
-ctgA	15078	.	T	A	96	.	DP=12;VDB=0.0404;AF1=1;AC1=2;DP4=0,0,4,8;MQ=37;FQ=-63	GT:PL:GQ	1/1:129,36,0:69
-ctgA	15163	.	gcc	gCcc	213	.	INDEL;DP=20;VDB=0.0404;AF1=1;AC1=2;DP4=0,0,10,7;MQ=37;FQ=-85.5	GT:PL:GQ	1/1:254,51,0:99
-ctgA	15418	.	A	G	64	.	DP=19;VDB=0.0253;AF1=0.5003;AC1=1;DP4=5,1,5,8;MQ=35;FQ=4.13;PV4=0.14,0.26,0.11,1	GT:PL:GQ	0/1:94,0,29:32
-ctgA	17042	.	C	T	119	.	DP=22;VDB=0.0394;AF1=1;AC1=2;DP4=0,0,13,9;MQ=37;FQ=-93	GT:PL:GQ	1/1:152,66,0:99
-ctgA	18948	.	A	G	57	.	DP=23;VDB=0.0308;AF1=0.5;AC1=1;DP4=6,4,4,9;MQ=37;FQ=39;PV4=0.22,1,0.2,1	GT:PL:GQ	0/1:87,0,66:69
-ctgA	19882	.	acg	a	98.5	.	INDEL;DP=22;VDB=0.0374;AF1=0.5;AC1=1;DP4=4,6,3,5;MQ=37;FQ=101;PV4=1,0.049,1,1	GT:PL:GQ	0/1:136,0,202:99
-ctgA	20675	.	T	C	40	.	DP=18;VDB=0.0401;AF1=0.5;AC1=1;DP4=5,3,4,6;MQ=36;FQ=31.7;PV4=0.64,1,0.19,0.15	GT:PL:GQ	0/1:70,0,59:62
-ctgA	21485	.	C	T,A	118	.	DP=20;VDB=0.0388;AF1=1;AC1=2;DP4=0,0,8,12;MQ=36;FQ=-84	GT:PL:GQ	1/1:151,57,0,150,42,147:99
-ctgA	22326	.	C	T	107	.	DP=14;VDB=0.0399;AF1=1;AC1=2;DP4=0,0,6,8;MQ=36;FQ=-69	GT:PL:GQ	1/1:140,42,0:81
-ctgA	23636	.	A	C	58	.	DP=19;VDB=0.0320;AF1=0.5;AC1=1;DP4=2,5,5,7;MQ=37;FQ=18.1;PV4=0.66,0.23,1,0.037	GT:PL:GQ	0/1:88,0,45:48
-ctgA	23959	.	A	G	118	.	DP=19;VDB=0.0374;AF1=1;AC1=2;DP4=0,0,7,11;MQ=36;FQ=-81	GT:PL:GQ	1/1:151,54,0:99
-ctgA	24978	.	C	G	127	.	DP=22;VDB=0.0355;AF1=1;AC1=2;DP4=0,0,11,11;MQ=35;FQ=-93	GT:PL:GQ	1/1:160,66,0:99
-ctgA	25558	.	A	C	104	.	DP=27;VDB=0.0371;AF1=1;AC1=2;DP4=0,0,18,7;MQ=36;FQ=-102	GT:PL:GQ	1/1:137,75,0:99
-ctgA	26079	.	C	A	29	.	DP=18;VDB=0.0339;AF1=0.5;AC1=1;DP4=6,4,4,4;MQ=36;FQ=31.9;PV4=1,0.14,0.44,0.13	GT:PL:GQ	0/1:59,0,76:62
-ctgA	28463	.	T	A	27	.	DP=20;VDB=0.0399;AF1=0.5;AC1=1;DP4=5,6,4,5;MQ=36;FQ=30;PV4=1,1,1,1	GT:PL:GQ	0/1:57,0,82:60
-ctgA	28719	.	T	G	39	.	DP=18;VDB=0.0333;AF1=0.5;AC1=1;DP4=6,3,5,4;MQ=37;FQ=36.6;PV4=1,1,1,1	GT:PL:GQ	0/1:69,0,65:67
-ctgA	29032	.	G	T	103	.	DP=19;VDB=0.0399;AF1=1;AC1=2;DP4=0,0,13,6;MQ=37;FQ=-84	GT:PL:GQ	1/1:136,57,0:99
-ctgA	29848	.	C	T	91	.	DP=11;VDB=0.0333;AF1=1;AC1=2;DP4=0,0,5,6;MQ=36;FQ=-60	GT:PL:GQ	1/1:124,33,0:63
-ctgA	34015	.	T	A	85	.	DP=10;VDB=0.0339;AF1=1;AC1=2;DP4=0,0,4,6;MQ=37;FQ=-57	GT:PL:GQ	1/1:118,30,0:57
-ctgA	35771	.	T	A	99	.	DP=16;VDB=0.0399;AF1=1;AC1=2;DP4=0,0,3,13;MQ=36;FQ=-75	GT:PL:GQ	1/1:132,48,0:93
-ctgA	38156	.	C	G	16.1	.	DP=12;VDB=0.0168;AF1=0.5;AC1=1;DP4=3,2,3,2;MQ=37;FQ=16.1;PV4=1,1,1,0.43	GT:PL:GQ	0/1:46,0,46:46
-ctgA	39952	.	C	T	124	.	DP=21;VDB=0.0404;AF1=1;AC1=2;DP4=0,0,11,10;MQ=33;FQ=-90	GT:PL:GQ	1/1:157,63,0:99
-ctgA	39966	.	T	C	11.3	.	DP=27;VDB=0.0299;AF1=0.5;AC1=1;DP4=11,5,2,7;MQ=34;FQ=14.2;PV4=0.041,1,0.01,1	GT:PL:GQ	0/1:41,0,88:43
-ctgA	39983	.	A	T	127	.	DP=24;VDB=0.0355;AF1=1;AC1=2;DP4=0,0,13,11;MQ=34;FQ=-99	GT:PL:GQ	1/1:160,72,0:99
-ctgA	41826	.	T	C	110	.	DP=18;VDB=0.0388;AF1=1;AC1=2;DP4=0,0,11,7;MQ=36;FQ=-81	GT:PL:GQ	1/1:143,54,0:99
-ctgA	42608	.	G	T	31	.	DP=24;VDB=0.0404;AF1=0.5;AC1=1;DP4=10,4,3,7;MQ=36;FQ=34;PV4=0.095,0.12,0.044,1	GT:PL:GQ	0/1:61,0,82:64
-ctgA	43007	.	T	A	36	.	DP=19;VDB=0.0355;AF1=0.5;AC1=1;DP4=3,5,9,2;MQ=36;FQ=30.4;PV4=0.074,1,0.11,1	GT:PL:GQ	0/1:66,0,58:60
-ctgA	43354	.	A	C	35	.	DP=20;VDB=0.0147;AF1=0.5;AC1=1;DP4=5,6,5,4;MQ=37;FQ=37.9;PV4=1,1,1,0.39	GT:PL:GQ	0/1:65,0,82:68
-ctgA	45666	.	G	T,A	91	.	DP=16;VDB=0.0388;AF1=1;AC1=2;DP4=0,0,10,6;MQ=36;FQ=-72	GT:PL:GQ	1/1:124,45,0,122,31,119:87
-ctgA	46994	.	T	A	40	.	DP=24;VDB=0.0308;AF1=0.5;AC1=1;DP4=6,7,7,4;MQ=37;FQ=43;PV4=0.44,1,1,0.49	GT:PL:GQ	0/1:70,0,89:73
-ctgA	47847	.	C	A,T	126	.	DP=23;VDB=0.0388;AF1=1;AC1=2;DP4=0,0,9,14;MQ=36;FQ=-93	GT:PL:GQ	1/1:159,66,0,158,51,155:99
-ctgA	48199	.	A	T	22	.	DP=17;VDB=0.0320;AF1=0.5;AC1=1;DP4=2,8,4,3;MQ=36;FQ=25;PV4=0.16,1,0.12,0.0062	GT:PL:GQ	0/1:52,0,71:55
-ctgA	49288	.	G	A	106	.	DP=23;VDB=0.0399;AF1=1;AC1=2;DP4=0,0,16,7;MQ=35;FQ=-96	GT:PL:GQ	1/1:139,69,0:99