Peromyscus maniculatus

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Resource Primary Assembly Alternate Assembly
GenBank mPerMan1: GCA_026229955.1 mPerMan1: GCA_026167925.1
ENA mPerMan1: GCA_026229955.1 mPerMan1: GCA_026167925.1
UCSC Genome Browser mPerMan1: GCA_026229955.1 mPerMan1: GCA_026167925.1

No image
Raw Data by Technology
Datatype Individual Bases Coverage Bytes Access
PacBio HiFi (.fq) mPerMan1 82.22 Gbp 29.07x 55.7 GiB
mPerMan3 193.03 Gbp 68.25x 90.1 GiB
PacBio HiFi (.bam) mPerMan3 196.41 Gbp 69.45x 648.2 GiB
Arima mPerMan3 235.64 Gbp 83.32x 127.4 GiB
Dovetail Genomics mPerMan1 74.81 Gbp 26.45x 35.5 GiB
Bases and Coverage are approximate.
Coverage based on genome size 2.83 Gbp.
Last upload on 19 August 2025.
Raw Data by Individual
Individual Datatype Bases Coverage Bytes Access
mPerMan1 PacBio HiFi (.fq) 82.22 Gbp 29.07x 55.7 GiB
Dovetail Genomics 74.81 Gbp 26.45x 35.5 GiB
mPerMan3 PacBio HiFi (.fq) 193.03 Gbp 68.25x 90.1 GiB
PacBio HiFi (.bam) 196.41 Gbp 69.45x 648.2 GiB
Arima 235.64 Gbp 83.32x 127.4 GiB
Bases and Coverage are approximate.
Coverage based on genome size 2.83 Gbp.
Last upload on 19 August 2025.
Assemblies
Individual 1 Primary Assembly
Version assembly_curated from 6 October 2025
mPerMan1.pri.cur.20251006.fasta.gz (787.4 MiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 9 25.75 Mbp 2 175.32 Mbp
20 21 21.01 Mbp 4 159.68 Mbp
30 37 15.63 Mbp 5 157.45 Mbp
40 57 13.14 Mbp 7 140.33 Mbp
50 81 10.71 Mbp 10 110.44 Mbp
60 110 8.41 Mbp 12 100.40 Mbp
70 149 6.25 Mbp 15 83.42 Mbp
80 203 3.97 Mbp 19 73.38 Mbp
90 302 1.95 Mbp 23 62.23 Mbp
100 2109 4.81 Kbp 1632 8.08 Kbp
1.000x 2109 2.83 Gbp 1632 2.83 Gbp
NG based on genome size 2.83 Gbp.
Individual 1 Alternate Assembly
Version assembly_curated from 6 October 2025
mPerMan1.alt.20251006.fasta.gz (742.3 MiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 5 39.36 Mbp 2 130.34 Mbp
20 15 24.09 Mbp 4 101.00 Mbp
30 27 18.80 Mbp 7 74.62 Mbp
40 44 13.96 Mbp 11 70.01 Mbp
50 64 12.29 Mbp 15 63.96 Mbp
60 88 9.36 Mbp 20 41.99 Mbp
70 122 6.82 Mbp 27 32.31 Mbp
80 166 4.81 Mbp 38 19.62 Mbp
90 241 2.60 Mbp 62 6.43 Mbp
100 1244 10.15 Kbp 1013 10.15 Kbp
1.000x 1244 2.65 Gbp 1013 2.65 Gbp
NG based on genome size 2.83 Gbp.
Individual 3 Haplotype 1 Assembly
Version assembly_vgp_HiC_2.0 from 10 October 2025
mPerMan3.HiC.hap1.20251010.fasta.gz (734.2 MiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 3 92.92 Mbp 2 173.68 Mbp
20 7 81.34 Mbp 4 149.85 Mbp
30 11 56.91 Mbp 6 144.50 Mbp
40 17 45.74 Mbp 8 123.14 Mbp
50 23 40.04 Mbp 10 110.09 Mbp
60 32 29.54 Mbp 13 94.57 Mbp
70 43 24.13 Mbp 17 78.05 Mbp
80 58 16.59 Mbp 20 73.36 Mbp
90 81 9.12 Mbp 25 45.74 Mbp
100 999 11.59 Kbp 910 11.59 Kbp
1.000x 999 2.92 Gbp 910 2.92 Gbp
NG based on genome size 2.83 Gbp.
Individual 3 Haplotype 2 Assembly
Version assembly_vgp_HiC_2.0 from 10 October 2025
mPerMan3.HiC.hap2.20251010.fasta.gz (676.7 MiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 3 90.44 Mbp 2 170.81 Mbp
20 6 83.05 Mbp 3 159.63 Mbp
30 10 65.52 Mbp 5 145.64 Mbp
40 15 48.41 Mbp 7 122.35 Mbp
50 21 39.71 Mbp 10 109.28 Mbp
60 28 31.77 Mbp 13 87.76 Mbp
70 38 25.26 Mbp 16 84.32 Mbp
80 51 17.45 Mbp 19 72.20 Mbp
90 73 9.63 Mbp 23 45.94 Mbp
100 613 8.20 Kbp 524 8.20 Kbp
1.000x 613 2.72 Gbp 524 2.72 Gbp
NG based on genome size 2.83 Gbp.
Individual 3 Mitochondrial Assembly
Version assembly_MT_rockefeller from 10 October 2025
mPerMan3.MT.20251010.fasta.gz (5.2 KiB)

Quality: not computed
Assembly Metadata
assembly_vgp_HiC_2.0/mPerMan3.yml (view)
species: Peromyscus maniculatus
specimem: mPerMan3
projects:
  - vgp
assembled_by_group: Rockefeller
data_location: S3
release_to: S3
combine_for_curation: true
hap1: s3://genomeark/species/Peromyscus_maniculatus/mPerMan3/assembly_vgp_HiC_2.0/mPerMan3.HiC.hap1.20251010.fasta.gz
hap2: s3://genomeark/species/Peromyscus_maniculatus/mPerMan3/assembly_vgp_HiC_2.0/mPerMan3.HiC.hap2.20251010.fasta.gz
pretext_hap1: s3://genomeark/species/Peromyscus_maniculatus/mPerMan3/assembly_vgp_HiC_2.0/evaluation/hap1/pretext/s2/mPerMan3_hap1__s2_heatmap.pretext
pretext_hap2: s3://genomeark/species/Peromyscus_maniculatus/mPerMan3/assembly_vgp_HiC_2.0/evaluation/hap2/pretext/s2/mPerMan3_hap2__s2_heatmap.pretext
kmer_spectra_img: s3://genomeark/species/Peromyscus_maniculatus/mPerMan3/assembly_vgp_HiC_2.0/evaluation/merqury/mPerMan3_png/
pacbio_read_dir: s3://genomeark/species/Peromyscus_maniculatus/mPerMan3/genomic_data/pacbio_hifi/
pacbio_read_type: hifi
hic_read_dir: s3://genomeark/species/Peromyscus_maniculatus/mPerMan3/genomic_data/arima/
pipeline:
  - hifiasm (0.25.0+galaxy0)
  - yahs (1.2a.2+galaxy2)
  - VGP0 mitoHiFi workflow (v0.2.2)
  - VGP1 genomic profiling workflow (v0.4)
  - VGP4 HiFi HiC assembly workflow (v0.3.12)
  - VGP8 HiC scaffolding workflow (v2.2) with mapq=10
  - VGP9 decontamination workflow unpublished using FCS (0.5.5+galaxy0) 
  - Pre-curation worklfow (v1.0beta6) with mapq=10
notes: This was a Hifiasm-HiC assembly of mPerMan3 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.