Peromyscus polionotus

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Raw Data by Technology
Datatype Individual Bases Coverage Bytes Access
PacBio HiFi (.fq) mPerPol1 203.10 Gbp N/A 88.5 GiB
PacBio HiFi (.bam) mPerPol1 206.58 Gbp N/A 669.6 GiB
Arima mPerPol1 168.80 Gbp N/A 90.6 GiB
Bases and Coverage are approximate.
Coverage based on genome size .
Last upload on 6 November 2025.
Raw Data by Individual
Individual Datatype Bases Coverage Bytes Access
mPerPol1 PacBio HiFi (.fq) 203.10 Gbp N/A 88.5 GiB
PacBio HiFi (.bam) 206.58 Gbp N/A 669.6 GiB
Arima 168.80 Gbp N/A 90.6 GiB
Bases and Coverage are approximate.
Coverage based on genome size .
Last upload on 6 November 2025.
Assemblies
Individual 1 Haplotype 1 Assembly
Version assembly_vgp_HiC_2.0 from 5 December 2025
mPerPol1.HiC.hap1.20251205.fasta.gz (662.2 MiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 2 157.01 Mbp 2 173.08 Mbp
20 4 118.01 Mbp 3 170.01 Mbp
30 6 103.96 Mbp 5 142.43 Mbp
40 9 81.91 Mbp 7 134.12 Mbp
50 12 77.12 Mbp 8 121.35 Mbp
60 15 70.63 Mbp 11 101.46 Mbp
70 19 55.35 Mbp 13 88.86 Mbp
80 25 32.57 Mbp 16 79.49 Mbp
90 35 16.44 Mbp 20 67.95 Mbp
100 373 15.71 Kbp 295 15.71 Kbp
1.000x 373 2.50 Gbp 295 2.50 Gbp
NG based on genome size .
Individual 1 Haplotype 2 Assembly
Version assembly_vgp_HiC_2.0 from 5 December 2025
mPerPol1.HiC.hap2.20251205.fasta.gz (707.4 MiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 2 124.60 Mbp 2 186.41 Mbp
20 5 105.86 Mbp 3 173.49 Mbp
30 7 99.90 Mbp 5 158.84 Mbp
40 10 89.05 Mbp 7 140.11 Mbp
50 14 73.27 Mbp 9 121.92 Mbp
60 18 62.07 Mbp 11 109.17 Mbp
70 22 55.53 Mbp 14 89.05 Mbp
80 27 47.23 Mbp 17 80.08 Mbp
90 37 18.60 Mbp 21 66.72 Mbp
100 289 21.44 Kbp 231 21.44 Kbp
1.000x 289 2.69 Gbp 231 2.69 Gbp
NG based on genome size .
Individual 1 Mitochondrial Assembly
Version assembly_MT_rockefeller from 5 December 2025
mPerPol1.MT.20251205.fasta.gz (5.2 KiB)

Quality: not computed
Assembly Metadata
assembly_vgp_HiC_2.0/mPerPol1.yml (view)
species: Peromyscus polionotus
specimem: mPerPol1
projects:
  - vgp
assembled_by_group: Rockefeller
data_location: S3
release_to: S3
combine_for_curation: true
hap1: s3://genomeark/species/Peromyscus_polionotus/mPerPol1/assembly_vgp_HiC_2.0/mPerPol1.HiC.hap1.20251205.fasta.gz
hap2: s3://genomeark/species/Peromyscus_polionotus/mPerPol1/assembly_vgp_HiC_2.0/mPerPol1.HiC.hap2.20251205.fasta.gz
pretext_hap1: s3://genomeark/species/Peromyscus_polionotus/mPerPol1/assembly_vgp_HiC_2.0/evaluation/hap1/pretext/s2/mPerPol1_hap1__s2_heatmap.pretext
pretext_hap2: s3://genomeark/species/Peromyscus_polionotus/mPerPol1/assembly_vgp_HiC_2.0/evaluation/hap2/pretext/s2/mPerPol1_hap2__s2_heatmap.pretext
kmer_spectra_img: s3://genomeark/species/Peromyscus_polionotus/mPerPol1/assembly_vgp_HiC_2.0/evaluation/merqury/mPerPol1_png/
pacbio_read_dir: s3://genomeark/species/Peromyscus_polionotus/mPerPol1/genomic_data/pacbio_hifi/
pacbio_read_type: hifi
hic_read_dir: s3://genomeark/species/Peromyscus_polionotus/mPerPol1/genomic_data/arima/
pipeline:
  - hifiasm (0.25.0+galaxy0)
  - yahs (1.2a.2+galaxy3)
  - VGP0 mitoHiFi workflow (v0.2.2)
  - VGP1 genomic profiling workflow (v0.6)
  - VGP4 HiFi HiC assembly workflow (v0.4)
  - VGP8 HiC scaffolding workflow (v3.2) with mapq=10
  - VGP9 decontamination workflow (v1.2) 
  - Pre-curation worklfow (v1.0beta6) with mapq=10
notes: This was a Hifiasm-HiC assembly of mPerPol1 resulting in two haplotype assemblies. HiC data were generated using the Arima library prep kit, and require trimming the first 5 bp off from the 5' end of both read files. The restriction enzymes used were the Arima v2 kit, so the cutting sites are GATC, GANTC, CTNAG, TTAA.
Data Use Policy

Samples and data come from a variety of sources. To support fair and productive use of this data, please abide by the Data Use Policy and contact Erich D. Jarvis, ejarvis@rockefeller.edu, with any questions.