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LD across an inversion (mosquitoes)

TL;DR: a 22 Mb inversion reads as one block, from plink2 --r2-phased output through an LDTrack. The same inversion also loads as a structural variant genotyped per mosquito.

Prerequisites

  • a JBrowse to paste the tracks into (Web or Desktop); every file here is a URL, so Desktop needs nothing hosted
  • PLINK 2.0 (plink2), labeled alpha for years despite being the version in general use
  • htslib (bgzip, tabix)
  • samtools
  • curl
  • python3
  • node, for the JBrowse CLI

Where the data comes from

Ag1000G phase 2 AR1 (Anopheles gambiae 1000 Genomes Consortium 2020), whose terms of use were lifted in March 2022, so nothing here needs registration or a data-access agreement.

The 2La inversion as one LD block

Two facts set up the page:

  • Crossing over is suppressed in a 2La heterokaryotype, so the segment travels as a unit. Gene flux still crosses it, away from the breakpoints.
  • The 2La inversion in Anopheles gambiae spans roughly 22 Mb of chromosome arm 2L, past what can be computed live from a VCF, so this LD is precomputed with PLINK and read through PlinkLDTabixAdapter.

The sections below build that table, load the same inversion genotyped per mosquito, and read the two together.

The LD is a file that plink2 --r2-phased writes in three steps: thin the variants, correlate them, index the table. keep.CMgam.txt is the population, two tab-separated columns of the same sample id, the family/individual pair plink asks for.

# the display uploads n(n-1)/2 cells, and ~800 SNPs across an arm is already at
# screen resolution, so keep roughly one variant per 50 kb rather than every
# variant the callset has
plink2 --bfile common --allow-extra-chr --keep keep.CMgam.txt --maf 0.2 \
  --chr 2L --write-snplist --out sel
awk -F'_' -v g=50000 '{p=$2+0; if (p >= nxt) {print $0; nxt = p + g}}' \
  sel.snplist > grid.snplist

# --r2-phased is the haplotype-frequency estimate rather than a correlation
# between dosages, which is what the display draws; dprimeabs adds D' beside it
# as a magnitude, which is how the display reads a precomputed cell.
# --ld-window-r2 0 keeps the uncorrelated pairs. On PLINK 1.9 the pair is one
# flag, `--r2 dprime`, and the columns come out at the same offsets.
plink2 --bfile common --allow-extra-chr --keep keep.CMgam.txt \
  --extract grid.snplist \
  --r2-phased cols=chrom,pos,id,dprimeabs \
  --ld-window 999999 --ld-window-kb 1000000 --ld-window-r2 0 \
  --out ag1000g_2L_CMgam

# plink2 writes tabs and comments its own header, which is what `tabix -H`
# returns. `sort-bed` is `sort -k1,1 -k2,2n` under LC_ALL=C with that `#` line
# kept on top, which is what this table wants too: same first two columns.
jbrowse sort-bed < ag1000g_2L_CMgam.vcor |
  bgzip > ag1000g_2L_CMgam.vcor.gz
tabix -s 1 -b 2 -e 2 -f ag1000g_2L_CMgam.vcor.gz

The track over that file is an LDTrack, and the display reads one of its two metric columns:

{
  "type": "LDTrack",
  "trackId": "ag1000g_2l_cmgam",
  "name": "Cameroon, both arrangements segregating (r²)",
  "assemblyNames": ["anoGam3"],
  "adapter": {
    "type": "PlinkLDTabixAdapter",
    "uri": "https://jbrowse.org/demos/popgen/ag1000g_2L_CMgam.vcor.gz"
  },
  "displays": [
    {
      "type": "LDTrackDisplay",
      "ldMetric": "r2",
      "useGenomicPositions": true,
      "showLegend": true,
      "height": 340
    }
  ]
}
jbrowse add-track-json '{
  "type": "LDTrack",
  "trackId": "ag1000g_2l_cmgam",
  "name": "Cameroon, both arrangements segregating (r²)",
  "assemblyNames": ["anoGam3"],
  "adapter": {
    "type": "PlinkLDTabixAdapter",
    "uri": "https://jbrowse.org/demos/popgen/ag1000g_2L_CMgam.vcor.gz"
  },
  "displays": [
    {
      "type": "LDTrackDisplay",
      "ldMetric": "r2",
      "useGenomicPositions": true,
      "showLegend": true,
      "height": 340
    }
  ]
}'

In JBrowse Desktop, or in any running JBrowse Web session, open a view on this track’s assembly, then File → Open track..., choose Add track from pasted JSON, and paste:

{
  "type": "LDTrack",
  "trackId": "ag1000g_2l_cmgam",
  "name": "Cameroon, both arrangements segregating (r²)",
  "assemblyNames": ["anoGam3"],
  "adapter": {
    "type": "PlinkLDTabixAdapter",
    "uri": "https://jbrowse.org/demos/popgen/ag1000g_2L_CMgam.vcor.gz"
  },
  "displays": [
    {
      "type": "LDTrackDisplay",
      "ldMetric": "r2",
      "useGenomicPositions": true,
      "showLegend": true,
      "height": 340
    }
  ]
}

The inversion genotyped per mosquito

The same inversion loads as one <INV> record spanning the breakpoints, genotyped across every mosquito. The regular multi-sample variant display draws each genotype at the call's true span, so a carrier's row begins and ends at the breakpoints.

Those genotypes are what the karyotype lanes in the figure below are: cells shaded by allele dosage, each lane sorted into standard, heterozygous and homozygous-inverted blocks. The karyotype column names the three classes by genotype, and so does the legend: 2L+a/2L+a, 2La/2L+a, 2La/2La, the + marking the non-inverted arrangement.

Load each population as a VariantTrack whose adapter carries the samples TSV, with a LinearMultiSampleVariantDisplay that orders (groupBy) and colors (colorBy) its rows by the karyotype column:

{
  "type": "VariantTrack",
  "trackId": "ag1000g_2la_karyotype_cmgam",
  "name": "Cameroon, one row per mosquito",
  "assemblyNames": ["anoGam3"],
  "adapter": {
    "type": "VcfTabixAdapter",
    "uri": "https://jbrowse.org/demos/popgen/ag1000g_2La_CMgam.vcf.gz",
    "samplesTsvLocation": {
      "uri": "https://jbrowse.org/demos/popgen/ag1000g_2La_CMgam_samples.tsv"
    }
  },
  "displays": [
    {
      "type": "LinearMultiSampleVariantDisplay",
      "groupBy": "karyotype",
      "colorBy": "karyotype",
      "referenceDrawingMode": "skip"
    }
  ]
}
jbrowse add-track-json '{
  "type": "VariantTrack",
  "trackId": "ag1000g_2la_karyotype_cmgam",
  "name": "Cameroon, one row per mosquito",
  "assemblyNames": ["anoGam3"],
  "adapter": {
    "type": "VcfTabixAdapter",
    "uri": "https://jbrowse.org/demos/popgen/ag1000g_2La_CMgam.vcf.gz",
    "samplesTsvLocation": {
      "uri": "https://jbrowse.org/demos/popgen/ag1000g_2La_CMgam_samples.tsv"
    }
  },
  "displays": [
    {
      "type": "LinearMultiSampleVariantDisplay",
      "groupBy": "karyotype",
      "colorBy": "karyotype",
      "referenceDrawingMode": "skip"
    }
  ]
}'

In JBrowse Desktop, or in any running JBrowse Web session, open a view on this track’s assembly, then File → Open track..., choose Add track from pasted JSON, and paste:

{
  "type": "VariantTrack",
  "trackId": "ag1000g_2la_karyotype_cmgam",
  "name": "Cameroon, one row per mosquito",
  "assemblyNames": ["anoGam3"],
  "adapter": {
    "type": "VcfTabixAdapter",
    "uri": "https://jbrowse.org/demos/popgen/ag1000g_2La_CMgam.vcf.gz",
    "samplesTsvLocation": {
      "uri": "https://jbrowse.org/demos/popgen/ag1000g_2La_CMgam_samples.tsv"
    }
  },
  "displays": [
    {
      "type": "LinearMultiSampleVariantDisplay",
      "groupBy": "karyotype",
      "colorBy": "karyotype",
      "referenceDrawingMode": "skip"
    }
  ]
}

What each setting does:

  • groupBy keeps the karyotype classes contiguous, so each class reads as one block.
  • referenceDrawingMode is on its default, skip, which fills the lane with the reference color and paints alt cells on top: a solid grey field with the carriers' blocks on it.

Rows divide the lane's height between them, so a 300-pixel lane gives each of 297 mosquitoes about a pixel. The display draws a row for every sample in the file, which makes each population its own track.

The karyotype calls

2La is a cytologically defined arrangement whose breakpoints have been cloned and sequenced (Sharakhov et al. 2006), and the call is drawn at that published extent. PCR across the junctions karyotypes single mosquitoes, checked against polytene cytology on field specimens (White et al. 2007).

Each mosquito's karyotype here is scored from those tag SNPs, the in-silico method MalariaGEN ships for the current Ag3 release: the mean number of alternate alleles across the tags, rounded into a genotype. That score comes out trimodal with empty space between the peaks, and the reproduce script prints the histogram and the karyotype breakdown per population.

The block on the karyotype lanes

Four lanes stack in the figure: each population's r² heatmap over its own karyotype lane, one row per mosquito, 297 from Cameroon and 69 from Gabon.

Ag1000G chromosome arm 2L, the same window and settings throughout. Top: the published extents of 2La and of Vgsc, the two loci the blocks below sit on. r² fills the 2La extent in the Cameroon panel, which segregates both arrangements, and is empty over that span in Gabon, which is near-fixed for the standard arrangement. Open this view in JBrowse ↗ (large dataset — this session takes a while to load)

The steps behind the figure above, run against your own data.

  1. Open your genome: on the JBrowse Desktop start screen click Open new genome (or Show all available genomes to pick a hosted one).This figure uses anoGam3.
  2. Add your own track: File → Open track..., then paste a URL or choose a local file. This one needs features defined inline in the config.This figure uses “2L loci”.
  3. Drag the bar at the bottom edge of the track to resize it.“2L loci”.
  4. Add your own track: File → Open track..., then paste a URL or choose a local file.This figure uses “Cameroon, both arrangements segregating (r²)”.
  5. Add your own track: File → Open track..., then paste a URL or choose a local file. This one needs a bgzip-compressed, tabix-indexed VCF (.vcf.gz + .tbi).This figure uses “Cameroon, one row per mosquito”.
  6. Add your own track: File → Open track..., then paste a URL or choose a local file.This figure uses “Gabon, one arrangement in almost every mosquito (r²)”.
  7. Add your own track: File → Open track..., then paste a URL or choose a local file. This one needs a bgzip-compressed, tabix-indexed VCF (.vcf.gz + .tbi).This figure uses “Gabon, one row per mosquito”.
  8. Type your region of interest into the location box and press Enter.This figure is at chr2L.

Open this view in JBrowse Desktop ↗

Opens JBrowse Desktop (JBrowse Desktop 5.0+) at this view and saves it as a reopenable session — swap in your own files afterwards.

Nothing happens? Paste this link into Desktop's Open JBrowse Web link... (start screen, or File → Session):

https://jbrowse.org/code/jb2/main/?config=https%3A%2F%2Fjbrowse.org%2Fucsc%2FanoGam3%2Fconfig.json&session=spec-%7B%22sessionTracks%22%3A%5B%7B%22type%22%3A%22FeatureTrack%22%2C%22trackId%22%3A%22ag1000g_2l_loci%22%2C%22name%22%3A%222L+loci%22%2C%22assemblyNames%22%3A%5B%22anoGam3%22%5D%2C%22adapter%22%3A%7B%22type%22%3A%22FromConfigAdapter%22%2C%22adapterId%22%3A%22ag1000g_2l_loci%22%2C%22features%22%3A%5B%7B%22uniqueId%22%3A%22vgsc%22%2C%22refName%22%3A%22chr2L%22%2C%22start%22%3A2358158%2C%22end%22%3A2431617%2C%22name%22%3A%22Vgsc%22%2C%22type%22%3A%22gene%22%7D%2C%7B%22uniqueId%22%3A%22two_la%22%2C%22refName%22%3A%22chr2L%22%2C%22start%22%3A20524058%2C%22end%22%3A42165532%2C%22name%22%3A%222La%22%2C%22type%22%3A%22inversion%22%7D%5D%7D%7D%2C%7B%22type%22%3A%22LDTrack%22%2C%22trackId%22%3A%22ag1000g_2l_cmgam%22%2C%22name%22%3A%22Cameroon%2C+both+arrangements+segregating+%28r%C2%B2%29%22%2C%22assemblyNames%22%3A%5B%22anoGam3%22%5D%2C%22adapter%22%3A%7B%22type%22%3A%22PlinkLDTabixAdapter%22%2C%22uri%22%3A%22https%3A%2F%2Fjbrowse.org%2Fdemos%2Fpopgen%2Fag1000g_2L_CMgam.ld.gz%22%7D%2C%22displays%22%3A%5B%7B%22type%22%3A%22LDTrackDisplay%22%2C%22ldMetric%22%3A%22r2%22%2C%22useGenomicPositions%22%3Atrue%2C%22showLegend%22%3Atrue%2C%22squashToHeight%22%3Afalse%2C%22height%22%3A340%7D%5D%7D%2C%7B%22type%22%3A%22VariantTrack%22%2C%22trackId%22%3A%22ag1000g_2la_karyotype_cmgam%22%2C%22name%22%3A%22Cameroon%2C+one+row+per+mosquito%22%2C%22assemblyNames%22%3A%5B%22anoGam3%22%5D%2C%22adapter%22%3A%7B%22type%22%3A%22VcfTabixAdapter%22%2C%22uri%22%3A%22https%3A%2F%2Fjbrowse.org%2Fdemos%2Fpopgen%2Fag1000g_2La_CMgam.vcf.gz%22%2C%22samplesTsvLocation%22%3A%7B%22uri%22%3A%22https%3A%2F%2Fjbrowse.org%2Fdemos%2Fpopgen%2Fag1000g_2La_CMgam_samples.tsv%22%7D%7D%2C%22displays%22%3A%5B%7B%22type%22%3A%22LinearMultiSampleVariantDisplay%22%2C%22groupBy%22%3A%22karyotype%22%2C%22colorBy%22%3A%22karyotype%22%2C%22referenceDrawingMode%22%3A%22skip%22%2C%22showLegend%22%3Atrue%2C%22height%22%3A200%7D%5D%7D%2C%7B%22type%22%3A%22LDTrack%22%2C%22trackId%22%3A%22ag1000g_2l_gagam%22%2C%22name%22%3A%22Gabon%2C+one+arrangement+in+almost+every+mosquito+%28r%C2%B2%29%22%2C%22assemblyNames%22%3A%5B%22anoGam3%22%5D%2C%22adapter%22%3A%7B%22type%22%3A%22PlinkLDTabixAdapter%22%2C%22uri%22%3A%22https%3A%2F%2Fjbrowse.org%2Fdemos%2Fpopgen%2Fag1000g_2L_GAgam.ld.gz%22%7D%2C%22displays%22%3A%5B%7B%22type%22%3A%22LDTrackDisplay%22%2C%22ldMetric%22%3A%22r2%22%2C%22useGenomicPositions%22%3Atrue%2C%22showLegend%22%3Atrue%2C%22squashToHeight%22%3Afalse%2C%22height%22%3A250%7D%5D%7D%2C%7B%22type%22%3A%22VariantTrack%22%2C%22trackId%22%3A%22ag1000g_2la_karyotype_gagam%22%2C%22name%22%3A%22Gabon%2C+one+row+per+mosquito%22%2C%22assemblyNames%22%3A%5B%22anoGam3%22%5D%2C%22adapter%22%3A%7B%22type%22%3A%22VcfTabixAdapter%22%2C%22uri%22%3A%22https%3A%2F%2Fjbrowse.org%2Fdemos%2Fpopgen%2Fag1000g_2La_GAgam.vcf.gz%22%2C%22samplesTsvLocation%22%3A%7B%22uri%22%3A%22https%3A%2F%2Fjbrowse.org%2Fdemos%2Fpopgen%2Fag1000g_2La_GAgam_samples.tsv%22%7D%7D%2C%22displays%22%3A%5B%7B%22type%22%3A%22LinearMultiSampleVariantDisplay%22%2C%22groupBy%22%3A%22karyotype%22%2C%22colorBy%22%3A%22karyotype%22%2C%22referenceDrawingMode%22%3A%22skip%22%2C%22showLegend%22%3Afalse%2C%22height%22%3A170%7D%5D%7D%5D%2C%22views%22%3A%5B%7B%22type%22%3A%22LinearGenomeView%22%2C%22assembly%22%3A%22anoGam3%22%2C%22loc%22%3A%22chr2L%22%2C%22tracks%22%3A%5B%7B%22trackId%22%3A%22ag1000g_2l_loci%22%2C%22type%22%3A%22LinearBasicDisplay%22%2C%22height%22%3A40%7D%2C%7B%22trackId%22%3A%22ag1000g_2l_cmgam%22%2C%22type%22%3A%22LDTrackDisplay%22%7D%2C%7B%22trackId%22%3A%22ag1000g_2la_karyotype_cmgam%22%2C%22type%22%3A%22LinearMultiSampleVariantDisplay%22%7D%2C%7B%22trackId%22%3A%22ag1000g_2l_gagam%22%2C%22type%22%3A%22LDTrackDisplay%22%7D%2C%7B%22trackId%22%3A%22ag1000g_2la_karyotype_gagam%22%2C%22type%22%3A%22LinearMultiSampleVariantDisplay%22%7D%5D%7D%5D%7D&sessionName=JBrowse+docs%3A+ld%2Fanopheles_2la

A figure adds its tracks to one session. The jbrowse CLI writes the same tracks into a config.json instead, where every session that opens it has them: add-track where flags cover the whole track, add-track-json where they do not.

jbrowse add-track-json '{
  "type": "FeatureTrack",
  "trackId": "ag1000g_2l_loci",
  "name": "2L loci",
  "assemblyNames": [
    "anoGam3"
  ],
  "adapter": {
    "type": "FromConfigAdapter",
    "adapterId": "ag1000g_2l_loci",
    "features": [
      {
        "uniqueId": "vgsc",
        "refName": "chr2L",
        "start": 2358158,
        "end": 2431617,
        "name": "Vgsc",
        "type": "gene"
      },
      {
        "uniqueId": "two_la",
        "refName": "chr2L",
        "start": 20524058,
        "end": 42165532,
        "name": "2La",
        "type": "inversion"
      }
    ]
  }
}'

jbrowse add-track-json '{
  "type": "LDTrack",
  "trackId": "ag1000g_2l_cmgam",
  "name": "Cameroon, both arrangements segregating (r²)",
  "assemblyNames": [
    "anoGam3"
  ],
  "adapter": {
    "type": "PlinkLDTabixAdapter",
    "uri": "https://jbrowse.org/demos/popgen/ag1000g_2L_CMgam.ld.gz"
  },
  "displays": [
    {
      "type": "LDTrackDisplay",
      "ldMetric": "r2",
      "useGenomicPositions": true,
      "showLegend": true,
      "squashToHeight": false,
      "height": 340
    }
  ]
}'

jbrowse add-track-json '{
  "type": "VariantTrack",
  "trackId": "ag1000g_2la_karyotype_cmgam",
  "name": "Cameroon, one row per mosquito",
  "assemblyNames": [
    "anoGam3"
  ],
  "adapter": {
    "type": "VcfTabixAdapter",
    "uri": "https://jbrowse.org/demos/popgen/ag1000g_2La_CMgam.vcf.gz",
    "samplesTsvLocation": {
      "uri": "https://jbrowse.org/demos/popgen/ag1000g_2La_CMgam_samples.tsv"
    }
  },
  "displays": [
    {
      "type": "LinearMultiSampleVariantDisplay",
      "groupBy": "karyotype",
      "colorBy": "karyotype",
      "referenceDrawingMode": "skip",
      "showLegend": true,
      "height": 200
    }
  ]
}'

jbrowse add-track-json '{
  "type": "LDTrack",
  "trackId": "ag1000g_2l_gagam",
  "name": "Gabon, one arrangement in almost every mosquito (r²)",
  "assemblyNames": [
    "anoGam3"
  ],
  "adapter": {
    "type": "PlinkLDTabixAdapter",
    "uri": "https://jbrowse.org/demos/popgen/ag1000g_2L_GAgam.ld.gz"
  },
  "displays": [
    {
      "type": "LDTrackDisplay",
      "ldMetric": "r2",
      "useGenomicPositions": true,
      "showLegend": true,
      "squashToHeight": false,
      "height": 250
    }
  ]
}'

jbrowse add-track-json '{
  "type": "VariantTrack",
  "trackId": "ag1000g_2la_karyotype_gagam",
  "name": "Gabon, one row per mosquito",
  "assemblyNames": [
    "anoGam3"
  ],
  "adapter": {
    "type": "VcfTabixAdapter",
    "uri": "https://jbrowse.org/demos/popgen/ag1000g_2La_GAgam.vcf.gz",
    "samplesTsvLocation": {
      "uri": "https://jbrowse.org/demos/popgen/ag1000g_2La_GAgam_samples.tsv"
    }
  },
  "displays": [
    {
      "type": "LinearMultiSampleVariantDisplay",
      "groupBy": "karyotype",
      "colorBy": "karyotype",
      "referenceDrawingMode": "skip",
      "showLegend": false,
      "height": 170
    }
  ]
}'

Run these where the config.json is, or add --out <dir>, and point each uri at your own file. The config needs anoGam3 already — jbrowse add-assembly adds yours. The location and the settings the steps carry are session state rather than track config — that half is the Session spec tab, or jbrowse set-default-session.

This session spec pastes after &session=spec- on any JBrowse Web instance.

{
  "sessionTracks": [
    {
      "type": "FeatureTrack",
      "trackId": "ag1000g_2l_loci",
      "name": "2L loci",
      "assemblyNames": [
        "anoGam3"
      ],
      "adapter": {
        "type": "FromConfigAdapter",
        "adapterId": "ag1000g_2l_loci",
        "features": [
          {
            "uniqueId": "vgsc",
            "refName": "chr2L",
            "start": 2358158,
            "end": 2431617,
            "name": "Vgsc",
            "type": "gene"
          },
          {
            "uniqueId": "two_la",
            "refName": "chr2L",
            "start": 20524058,
            "end": 42165532,
            "name": "2La",
            "type": "inversion"
          }
        ]
      }
    },
    {
      "type": "LDTrack",
      "trackId": "ag1000g_2l_cmgam",
      "name": "Cameroon, both arrangements segregating (r²)",
      "assemblyNames": [
        "anoGam3"
      ],
      "adapter": {
        "type": "PlinkLDTabixAdapter",
        "uri": "https://jbrowse.org/demos/popgen/ag1000g_2L_CMgam.ld.gz"
      },
      "displays": [
        {
          "type": "LDTrackDisplay",
          "ldMetric": "r2",
          "useGenomicPositions": true,
          "showLegend": true,
          "squashToHeight": false,
          "height": 340
        }
      ]
    },
    {
      "type": "VariantTrack",
      "trackId": "ag1000g_2la_karyotype_cmgam",
      "name": "Cameroon, one row per mosquito",
      "assemblyNames": [
        "anoGam3"
      ],
      "adapter": {
        "type": "VcfTabixAdapter",
        "uri": "https://jbrowse.org/demos/popgen/ag1000g_2La_CMgam.vcf.gz",
        "samplesTsvLocation": {
          "uri": "https://jbrowse.org/demos/popgen/ag1000g_2La_CMgam_samples.tsv"
        }
      },
      "displays": [
        {
          "type": "LinearMultiSampleVariantDisplay",
          "groupBy": "karyotype",
          "colorBy": "karyotype",
          "referenceDrawingMode": "skip",
          "showLegend": true,
          "height": 200
        }
      ]
    },
    {
      "type": "LDTrack",
      "trackId": "ag1000g_2l_gagam",
      "name": "Gabon, one arrangement in almost every mosquito (r²)",
      "assemblyNames": [
        "anoGam3"
      ],
      "adapter": {
        "type": "PlinkLDTabixAdapter",
        "uri": "https://jbrowse.org/demos/popgen/ag1000g_2L_GAgam.ld.gz"
      },
      "displays": [
        {
          "type": "LDTrackDisplay",
          "ldMetric": "r2",
          "useGenomicPositions": true,
          "showLegend": true,
          "squashToHeight": false,
          "height": 250
        }
      ]
    },
    {
      "type": "VariantTrack",
      "trackId": "ag1000g_2la_karyotype_gagam",
      "name": "Gabon, one row per mosquito",
      "assemblyNames": [
        "anoGam3"
      ],
      "adapter": {
        "type": "VcfTabixAdapter",
        "uri": "https://jbrowse.org/demos/popgen/ag1000g_2La_GAgam.vcf.gz",
        "samplesTsvLocation": {
          "uri": "https://jbrowse.org/demos/popgen/ag1000g_2La_GAgam_samples.tsv"
        }
      },
      "displays": [
        {
          "type": "LinearMultiSampleVariantDisplay",
          "groupBy": "karyotype",
          "colorBy": "karyotype",
          "referenceDrawingMode": "skip",
          "showLegend": false,
          "height": 170
        }
      ]
    }
  ],
  "views": [
    {
      "type": "LinearGenomeView",
      "assembly": "anoGam3",
      "loc": "chr2L",
      "tracks": [
        {
          "trackId": "ag1000g_2l_loci",
          "type": "LinearBasicDisplay",
          "height": 40
        },
        {
          "trackId": "ag1000g_2l_cmgam",
          "type": "LDTrackDisplay"
        },
        {
          "trackId": "ag1000g_2la_karyotype_cmgam",
          "type": "LinearMultiSampleVariantDisplay"
        },
        {
          "trackId": "ag1000g_2l_gagam",
          "type": "LDTrackDisplay"
        },
        {
          "trackId": "ag1000g_2la_karyotype_gagam",
          "type": "LinearMultiSampleVariantDisplay"
        }
      ]
    }
  ]
}

Loaded against config: https://jbrowse.org/ucsc/anoGam3/config.json

The same view with jbrowse-anywidget. Point the adapter at your own file.

from jbrowse_anywidget import LinearGenomeView, make_assembly

view = LinearGenomeView(
    assembly=make_assembly("anoGam3", "https://your-server/your-genome.fa.gz"),
    location="chr2L",
)

view.add_track({
    "type": "FeatureTrack",
    "trackId": "my_track_1",
    "name": "My track 1",
    "assemblyNames": ["anoGam3"],
    "adapter": {"type": "FromConfigAdapter", "uri": "https://your-server/your-file"},
})
view.add_track({
    "type": "LDTrack",
    "trackId": "my_track_2",
    "name": "My track 2",
    "assemblyNames": ["anoGam3"],
    "adapter": {"type": "PlinkLDTabixAdapter", "uri": "https://your-server/your-file"},
})
view.add_track({
    "type": "VariantTrack",
    "trackId": "my_track_3",
    "name": "My track 3",
    "assemblyNames": ["anoGam3"],
    "adapter": {"type": "VcfTabixAdapter", "uri": "https://your-server/your-file"},
})
view.add_track({
    "type": "LDTrack",
    "trackId": "my_track_4",
    "name": "My track 4",
    "assemblyNames": ["anoGam3"],
    "adapter": {"type": "PlinkLDTabixAdapter", "uri": "https://your-server/your-file"},
})
view.add_track({
    "type": "VariantTrack",
    "trackId": "my_track_5",
    "name": "My track 5",
    "assemblyNames": ["anoGam3"],
    "adapter": {"type": "VcfTabixAdapter", "uri": "https://your-server/your-file"},
})

view  # display the widget

Hand this to a coding agent. It rebuilds the figure above headlessly, and the session file is then the thing to edit — swap an adapter uri for your own file and rerun.

cat > session.json <<'JSON'
{
  "sessionTracks": [
    {
      "type": "FeatureTrack",
      "trackId": "ag1000g_2l_loci",
      "name": "2L loci",
      "assemblyNames": [
        "anoGam3"
      ],
      "adapter": {
        "type": "FromConfigAdapter",
        "adapterId": "ag1000g_2l_loci",
        "features": [
          {
            "uniqueId": "vgsc",
            "refName": "chr2L",
            "start": 2358158,
            "end": 2431617,
            "name": "Vgsc",
            "type": "gene"
          },
          {
            "uniqueId": "two_la",
            "refName": "chr2L",
            "start": 20524058,
            "end": 42165532,
            "name": "2La",
            "type": "inversion"
          }
        ]
      }
    },
    {
      "type": "LDTrack",
      "trackId": "ag1000g_2l_cmgam",
      "name": "Cameroon, both arrangements segregating (r²)",
      "assemblyNames": [
        "anoGam3"
      ],
      "adapter": {
        "type": "PlinkLDTabixAdapter",
        "uri": "https://jbrowse.org/demos/popgen/ag1000g_2L_CMgam.ld.gz"
      },
      "displays": [
        {
          "type": "LDTrackDisplay",
          "ldMetric": "r2",
          "useGenomicPositions": true,
          "showLegend": true,
          "squashToHeight": false,
          "height": 340
        }
      ]
    },
    {
      "type": "VariantTrack",
      "trackId": "ag1000g_2la_karyotype_cmgam",
      "name": "Cameroon, one row per mosquito",
      "assemblyNames": [
        "anoGam3"
      ],
      "adapter": {
        "type": "VcfTabixAdapter",
        "uri": "https://jbrowse.org/demos/popgen/ag1000g_2La_CMgam.vcf.gz",
        "samplesTsvLocation": {
          "uri": "https://jbrowse.org/demos/popgen/ag1000g_2La_CMgam_samples.tsv"
        }
      },
      "displays": [
        {
          "type": "LinearMultiSampleVariantDisplay",
          "groupBy": "karyotype",
          "colorBy": "karyotype",
          "referenceDrawingMode": "skip",
          "showLegend": true,
          "height": 200
        }
      ]
    },
    {
      "type": "LDTrack",
      "trackId": "ag1000g_2l_gagam",
      "name": "Gabon, one arrangement in almost every mosquito (r²)",
      "assemblyNames": [
        "anoGam3"
      ],
      "adapter": {
        "type": "PlinkLDTabixAdapter",
        "uri": "https://jbrowse.org/demos/popgen/ag1000g_2L_GAgam.ld.gz"
      },
      "displays": [
        {
          "type": "LDTrackDisplay",
          "ldMetric": "r2",
          "useGenomicPositions": true,
          "showLegend": true,
          "squashToHeight": false,
          "height": 250
        }
      ]
    },
    {
      "type": "VariantTrack",
      "trackId": "ag1000g_2la_karyotype_gagam",
      "name": "Gabon, one row per mosquito",
      "assemblyNames": [
        "anoGam3"
      ],
      "adapter": {
        "type": "VcfTabixAdapter",
        "uri": "https://jbrowse.org/demos/popgen/ag1000g_2La_GAgam.vcf.gz",
        "samplesTsvLocation": {
          "uri": "https://jbrowse.org/demos/popgen/ag1000g_2La_GAgam_samples.tsv"
        }
      },
      "displays": [
        {
          "type": "LinearMultiSampleVariantDisplay",
          "groupBy": "karyotype",
          "colorBy": "karyotype",
          "referenceDrawingMode": "skip",
          "showLegend": false,
          "height": 170
        }
      ]
    }
  ],
  "views": [
    {
      "type": "LinearGenomeView",
      "assembly": "anoGam3",
      "loc": "chr2L",
      "tracks": [
        {
          "trackId": "ag1000g_2l_loci",
          "type": "LinearBasicDisplay",
          "height": 40
        },
        {
          "trackId": "ag1000g_2l_cmgam",
          "type": "LDTrackDisplay"
        },
        {
          "trackId": "ag1000g_2la_karyotype_cmgam",
          "type": "LinearMultiSampleVariantDisplay"
        },
        {
          "trackId": "ag1000g_2l_gagam",
          "type": "LDTrackDisplay"
        },
        {
          "trackId": "ag1000g_2la_karyotype_gagam",
          "type": "LinearMultiSampleVariantDisplay"
        }
      ]
    }
  ]
}
JSON

npx @jbrowse/capture --instance https://jbrowse.org/code/jb2/main/ \
  --config https://jbrowse.org/ucsc/anoGam3/config.json \
  --session session.json -o figure.png

Using JBrowse with AI agents covers the rest: hosted genomes to point it at, and why waiting for the render is the part that goes wrong.

The block's edges land on the published breakpoint coordinates, and on the karyotype lane beneath the heatmap, whose cells are drawn at those same coordinates from a different file. Markers at opposite ends read about as correlated as neighbouring ones, at one variant per 50 kb above a 0.2 MAF floor.

Two more things stand out beyond the 2La block itself:

  • The second block is Vgsc. At the low-coordinate end of the arm in both panels, it is reddest along the diagonal and pales away below it: the sodium channel whose codon-995 substitutions confer pyrethroid resistance, and which this release was used to survey (Clarkson et al. 2021). Gabon shows that block too.
  • Gabon's 2La span reads flat. It is near-fixed for the standard arrangement, so almost no chromosome pair there is a heterokaryotype and nothing suppresses crossing over across the span. The few 2La chromosomes it does carry fall below the MAF floor with the variants that tag them.

Which metric recovers the breakpoints

D' saturates wherever no recombinant haplotype has turned up, so it reads on where crossing over stops rather than on how well one marker predicts another. That is what the reproduce script switches to recover the 2La breakpoints from the table, and the guide has both metrics and the allele-frequency floor beside them.

Reproduce it end to end

build_ag1000g_ld.sh does the whole build for you:

  • downloads the phased haplotypes
  • prints the long-range D' profile the breakpoints come off, the 2La score distribution and the karyotype breakdown per population
  • builds the tabix-indexed .vcor.gz tracks and the per-mosquito karyotype calls
  • writes a config.json opening on the inversion
curl -fO https://raw.githubusercontent.com/GMOD/jbrowse-components/main/scripts/build_ag1000g_ld.sh
bash build_ag1000g_ld.sh              # writes ./ag1000g_ld_build/jbrowse2
npx --yes serve ag1000g_ld_build/jbrowse2

The same karyotype track in Drosophila

Selection scans (Drosophila DGRP) builds the same one-record karyotype track for an 11 Mb Drosophila inversion.

See also

References