Microtus pennsylvanicus

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Raw Data by Technology
Datatype Individual Bases Coverage Bytes Access
PacBio HiFi (.fq) mMicPen1 96.59 Gbp N/A 80.5 GiB
Arima mMicPen1 274.30 Gbp N/A 151.2 GiB
Bases and Coverage are approximate.
Coverage based on genome size .
Last upload on 17 May 2023.
Raw Data by Individual
Individual Datatype Bases Coverage Bytes Access
mMicPen1 PacBio HiFi (.fq) 96.59 Gbp N/A 80.5 GiB
Arima 274.30 Gbp N/A 151.2 GiB
Bases and Coverage are approximate.
Coverage based on genome size .
Last upload on 17 May 2023.
Assemblies
Individual 1 Haplotype 1 Assembly
Version assembly_curated from 10 July 2023
mMicPen1.hap1.decontam.20230710.fasta.gz (583.0 MiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 2 108.68 Mbp 1 222.66 Mbp
20 4 97.27 Mbp 3 145.90 Mbp
30 7 71.35 Mbp 4 145.66 Mbp
40 11 52.61 Mbp 6 128.93 Mbp
50 15 47.18 Mbp 8 113.64 Mbp
60 20 40.99 Mbp 10 104.24 Mbp
70 26 36.77 Mbp 12 96.37 Mbp
80 33 27.94 Mbp 15 73.64 Mbp
90 42 17.81 Mbp 19 41.04 Mbp
100 229 14.95 Kbp 187 14.95 Kbp
1.000x 229 2.22 Gbp 187 2.22 Gbp
NG based on genome size .
Individual 1 Haplotype 2 Assembly
Version assembly_curated from 10 July 2023
mMicPen1.hap2.decontam.20230710.fasta.gz (613.1 MiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 3 104.29 Mbp 2 153.43 Mbp
20 5 97.56 Mbp 3 145.95 Mbp
30 8 79.77 Mbp 5 144.50 Mbp
40 11 68.64 Mbp 6 138.93 Mbp
50 14 60.46 Mbp 8 125.72 Mbp
60 19 44.21 Mbp 10 114.34 Mbp
70 24 37.49 Mbp 12 104.29 Mbp
80 32 27.00 Mbp 15 75.43 Mbp
90 43 14.22 Mbp 19 43.76 Mbp
100 207 11.26 Kbp 155 11.26 Kbp
1.000x 207 2.31 Gbp 155 2.31 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.