Microtus pennsylvanicus

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Resource Primary Assembly Alternate Assembly
GenBank mMicPen1: GCA_037038515.1 mMicPen1: GCA_037039175.1
ENA mMicPen1: GCA_037038515.1 mMicPen1: GCA_037039175.1
UCSC Genome Browser mMicPen1: GCA_037038515.1 mMicPen1: GCA_037039175.1

No image
Raw Data by Technology
Datatype Individual Bases Coverage Bytes Access
PacBio HiFi (subreads) mMicPen1 1913.27 Gbp N/A 3.3 TiB
PacBio HiFi (.fq) mMicPen1 96.59 Gbp N/A 80.5 GiB
PacBio HiFi (.bam) mMicPen1 305.95 Gbp N/A 1.1 TiB
Arima mMicPen1 274.30 Gbp N/A 151.2 GiB
Bases and Coverage are approximate.
Coverage based on genome size .
Last upload on 8 June 2024.
Raw Data by Individual
Individual Datatype Bases Coverage Bytes Access
mMicPen1 PacBio HiFi (subreads) 1913.27 Gbp N/A 3.3 TiB
PacBio HiFi (.fq) 96.59 Gbp N/A 80.5 GiB
PacBio HiFi (.bam) 305.95 Gbp N/A 1.1 TiB
Arima 274.30 Gbp N/A 151.2 GiB
Bases and Coverage are approximate.
Coverage based on genome size .
Last upload on 8 June 2024.
Assemblies
Individual 1 Haplotype 1 Assembly
Version assembly_curated from 10 July 2023
mMicPen1.hap1.cur.20230710.fa.gz (677.1 MiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 2 108.68 Mbp 2 153.58 Mbp
20 5 85.17 Mbp 3 145.90 Mbp
30 8 66.93 Mbp 5 144.50 Mbp
40 12 52.61 Mbp 6 139.30 Mbp
50 16 47.18 Mbp 8 125.31 Mbp
60 22 40.01 Mbp 10 113.64 Mbp
70 28 33.85 Mbp 13 98.93 Mbp
80 36 27.36 Mbp 15 76.40 Mbp
90 48 15.57 Mbp 20 42.43 Mbp
100 240 14.95 Kbp 180 14.95 Kbp
1.000x 240 2.37 Gbp 180 2.37 Gbp
NG based on genome size .
Individual 1 Haplotype 2 Assembly
Version assembly_curated from 10 July 2023
mMicPen1.hap2.cur.20230710.fa.gz (572.1 MiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 2 104.98 Mbp 1 222.09 Mbp
20 5 97.56 Mbp 3 145.95 Mbp
30 7 82.90 Mbp 4 145.71 Mbp
40 10 72.18 Mbp 6 132.05 Mbp
50 13 63.58 Mbp 8 118.37 Mbp
60 17 45.54 Mbp 9 114.34 Mbp
70 22 39.32 Mbp 11 105.61 Mbp
80 28 29.68 Mbp 14 75.43 Mbp
90 37 16.49 Mbp 17 46.33 Mbp
100 196 11.26 Kbp 143 11.26 Kbp
1.000x 196 2.16 Gbp 143 2.16 Gbp
NG based on genome size .
Individual 1 Mitochondrial Assembly
Version assembly_MT_rockefeller from 10 July 2023
mMicPen1.MT.20230710.fasta.gz (5.2 KiB)

Quality: not computed
Assembly Metadata
assembly_vgp_HiC_2.0/mMicPen1.yml (view)
species: Microtus pennsylvanicus
specimen: mMicPen1
projects: 
  - vgp
hap1: s3://genomeark/species/Microtus_pennsylvanicus/mMicPen1/assembly_vgp_HiC_2.0/mMicPen1.HiC.hap1.20230710.fasta.gz
hap2: s3://genomeark/species/Microtus_pennsylvanicus/mMicPen1/assembly_vgp_HiC_2.0/mMicPen1.HiC.hap2.20230710.fasta.gz
pretext_hap1: s3://genomeark/species/Microtus_pennsylvanicus/mMicPen1/assembly_vgp_HiC_2.0/evaluation/hap1/pretext/mMicPen1_hap1__s2_heatmap.pretext
pretext_hap2: s3://genomeark/species/Microtus_pennsylvanicus/mMicPen1/assembly_vgp_HiC_2.0/evaluation/hap2/pretext/mMicPen1_hap2__s2_heatmap.pretext
kmer_spectra_img: s3://genomeark/species/Microtus_pennsylvanicus/mMicPen1/assembly_vgp_HiC_2.0/evaluation/merqury/mMicPen1_png/
mito: s3://genomeark/species/Microtus_pennsylvanicus/mMicPen1/assembly_MT_rockefeller/mMicPen1.MT.20230710.fasta.gz
pipeline:
  - hifiasm (0.19.3+galaxy0)
  - yahs (1.2a.2+galaxy1)
assembled_by_group: Rockefeller
notes: This was a hifiasm-HiC assembly of mMicPen1, resulting in two complete haplotypes. This individual did not bionano data. HiC scaffolding was performed with yahs. The HiC prep was Arima kit 2. The HiC reads needed to have 5 bp trimmed from the 5' end due to adapter left over from the Arima library prep kit.
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.