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Genome assemblies

mMicOch_UCD_v1_hap1.fasta.gz

Prairie vole (Microtus ochrogaster), 26 autosomes plus X and Y. ERZ29502723

FASTA

720.6 MB

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mMicOch_UCD_v1_hap2.fasta.gz

Prairie vole, second haplotype. ERZ29502724

FASTA

658.1 MB

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mMicPen_UCD_v1_hap1.fasta.gz

Meadow vole (Microtus pennsylvanicus), 22 autosomes plus X and Y. ERZ29502725

FASTA

676.3 MB

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mMicPen_UCD_v1_hap2.fasta.gz

Meadow vole, second haplotype. ERZ29502726

FASTA

618.4 MB

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Gene annotation

prairie_hap1_egapx.gff.gz

First EGAPx round, short-read RNA-seq evidence only. Superseded by v2; use it only to reproduce earlier results.

GFF

13.6 MB

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prairie/complete.genomic.gff.gz

EGAPx v2 on prairie vole hap1. NCBI convention, with mRNA, exon, and CDS features.

GFF

14.8 MB

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prairie/complete.genomic.with_utrs.gff.gz

The same models with UTR features added by AGAT, for tools that expect them.

GFF

16.1 MB

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meadow_hap1_egapx.gff.gz

First EGAPx round, short-read RNA-seq evidence only. Superseded by v2.

GFF

15.6 MB

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meadow/complete.genomic.gff.gz

EGAPx v2 on meadow vole hap1. NCBI convention, with mRNA, exon, and CDS features.

GFF

17.2 MB

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meadow/complete.genomic.with_utrs.gff.gz

The same models with UTR features added by AGAT.

GFF

19.0 MB

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Sequencing reads

PRJEB89367

Prairie vole brain, liver, testes, and embryo RNA-seq. PRJEB89367

READS

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NCBI ENA

PRJEB108798

HiFi, CiFi, Hi-C, and Illumina WGS for both species and the woodland vole. PRJEB108798

READS

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NCBI ENA

Liftover chains

prairie_vole_mMicOch_UCD_vs_Broad_MicOch1.0.liftover_chains.tar.gz

Convert to the previous prairie reference GCF_000317375.1.

CHAIN

23.7 MB

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meadow_UCD_v1_to_VGP.liftover_chains.tar.gz

Convert to the VGP meadow reference GCF_037038515.1.

CHAIN

22.1 MB

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Chromatin contact maps

prairie_hap1.hic

CiFi proximity-ligation contacts on prairie hap1.

HIC

135.6 MB

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prairie_hap1.shortread_hic.hic

Proximo Hi-C contacts on prairie hap1.

HIC

273.3 MB

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meadow_hap1.shortread_hic.hic

Proximo Hi-C contacts on meadow hap1.

HIC

480.8 MB

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Browser tracks

Repeats, duplications and orthologs6 files

repeatmasker_detailed.bb

RepeatMasker annotations, colored by repeat class.

BIGBED

1.6 MB

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sedef_sd_bed.bb

SDs >1 kb at >90% identity, with mate coordinates.

BIGBED

3.3 MB

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prairie_orthologs.bb

Prairie and meadow ortholog groups, colored by copy-number relationship.

BIGBED

912 KB

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repeatmasker_detailed.bb

RepeatMasker annotations, colored by repeat class.

BIGBED

735 KB

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sedef_sd_bed.bb

SDs >1 kb at >90% identity, with mate coordinates.

BIGBED

4.6 MB

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meadow_orthologs.bb

Prairie and meadow ortholog groups, colored by copy-number relationship.

BIGBED

938 KB

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Methylation and read depth6 files

prairie_hap1.cpg_methylation.bw

5mC fraction from HiFi reads.

BIGWIG

22.2 MB

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prairie_hap1.hifi_coverage.bw

PacBio HiFi read depth.

BIGWIG

19.4 MB

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prairie_hap1.hic_coverage.bw

Proximo Hi-C read depth.

BIGWIG

18.7 MB

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meadow_hap1.cpg_methylation.bw

5mC fraction from HiFi reads.

BIGWIG

20.8 MB

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meadow_hap1.hifi_coverage.bw

PacBio HiFi read depth.

BIGWIG

18.1 MB

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meadow_hap1.hic_coverage.bw

Proximo Hi-C read depth.

BIGWIG

17.7 MB

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Copy number across seven vole species, prairie assembly7 files

prairie.CN.bw

Prairie vole (M. ochrogaster) read depth on the prairie assembly.

BIGWIG

7.4 MB

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meadow.CN.bw

Meadow vole (M. pennsylvanicus) read depth on the prairie assembly.

BIGWIG

7.4 MB

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montane.CN.bw

Montane vole (M. montanus) read depth on the prairie assembly.

BIGWIG

7.4 MB

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common.CN.bw

Common vole (M. arvalis) read depth on the prairie assembly.

BIGWIG

7.4 MB

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field.CN.bw

Field vole (M. agrestis) read depth on the prairie assembly.

BIGWIG

7.5 MB

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pine.CN.bw

Pine vole (M. pinetorum) read depth on the prairie assembly.

BIGWIG

7.4 MB

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water.CN.bw

Water vole (Arvicola amphibius) read depth on the prairie assembly.

BIGWIG

7.5 MB

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Copy number across seven vole species, meadow assembly7 files

prairie.CN.bw

Prairie vole (M. ochrogaster) read depth on the meadow assembly.

BIGWIG

7.4 MB

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meadow.CN.bw

Meadow vole (M. pennsylvanicus) read depth on the meadow assembly.

BIGWIG

7.4 MB

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montane.CN.bw

Montane vole (M. montanus) read depth on the meadow assembly.

BIGWIG

7.4 MB

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common.CN.bw

Common vole (M. arvalis) read depth on the meadow assembly.

BIGWIG

7.4 MB

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field.CN.bw

Field vole (M. agrestis) read depth on the meadow assembly.

BIGWIG

7.4 MB

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pine.CN.bw

Pine vole (M. pinetorum) read depth on the meadow assembly.

BIGWIG

7.4 MB

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water.CN.bw

Water vole (Arvicola amphibius) read depth on the meadow assembly.

BIGWIG

7.4 MB

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Assembly QC: gaps, telomeres and centromeres6 files

gaps.bb

Assembly gaps on the prairie assembly.

BIGBED

23 KB

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telomeres.bb

Telomere positions on the prairie assembly.

BIGBED

24 KB

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centromere_regions.bb

Centromere regions on the prairie assembly.

BIGBED

23 KB

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gaps.bb

Assembly gaps on the meadow assembly.

BIGBED

22 KB

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telomeres.bb

Telomere positions on the meadow assembly.

BIGBED

38 KB

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centromere_regions.bb

Centromere regions on the meadow assembly.

BIGBED

29 KB

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