Lagopus muta

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Resource Primary Assembly Alternate Assembly
GenBank bLagMut1: GCA_023343835.1 bLagMut1: GCA_023344045.1
ENA bLagMut1: GCA_023343835.1 bLagMut1: GCA_023344045.1
UCSC Genome Browser bLagMut1: GCA_023343835.1 bLagMut1: GCA_023344045.1

No image
Raw Data by Technology
Datatype Individual Bases Coverage Bytes Access
PacBio HiFi (subreads) bLagMut1 189.70 Gbp 184.75x 103.4 GiB
PacBio HiFi (.fq) bLagMut1 58.83 Gbp 57.30x 58.0 GiB
Dovetail Genomics bLagMut1 314.77 Gbp 306.57x 148.4 GiB
Bases and Coverage are approximate.
Coverage based on genome size 1.03 Gbp.
Last upload on 3 May 2022.
Raw Data by Individual
Individual Datatype Bases Coverage Bytes Access
bLagMut1 PacBio HiFi (subreads) 189.70 Gbp 184.75x 103.4 GiB
PacBio HiFi (.fq) 58.83 Gbp 57.30x 58.0 GiB
Dovetail Genomics 314.77 Gbp 306.57x 148.4 GiB
Bases and Coverage are approximate.
Coverage based on genome size 1.03 Gbp.
Last upload on 3 May 2022.
Assemblies
Individual 1 Primary Assembly
Version assembly_curated from 9 December 2021
bLagMut1.pri.cur.20211209.fasta.gz (295.9 MiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 2 39.94 Mbp 0 194.91 Mbp
20 5 31.74 Mbp 1 110.44 Mbp
30 8 27.99 Mbp 2 94.58 Mbp
40 13 19.85 Mbp 3 75.34 Mbp
50 18 17.91 Mbp 4 71.23 Mbp
60 24 16.49 Mbp 6 59.59 Mbp
70 30 14.46 Mbp 7 51.91 Mbp
80 41 7.41 Mbp 11 19.85 Mbp
90 63 2.85 Mbp 18 10.90 Mbp
100 373 171 bp 163 2.26 Kbp
1.000x 374 1.03 Gbp 164 1.03 Gbp
NG based on genome size 1.03 Gbp.
Individual 1 Alternate Assembly
Version assembly_curated from 9 December 2021
bLagMut1.alt.cur.20211209.fasta.gz (268.4 MiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 33 1.84 Mbp 33 1.84 Mbp
20 94 1.30 Mbp 94 1.30 Mbp
30 175 1.00 Mbp 175 1.00 Mbp
40 280 0.78 Mbp 280 0.78 Mbp
50 413 0.62 Mbp 412 0.62 Mbp
60 582 477.52 Kbp 581 477.84 Kbp
70 805 359.72 Kbp 804 360.16 Kbp
80 1117 248.27 Kbp 1115 249.53 Kbp
90 1623 129.60 Kbp 1619 131.22 Kbp
100 3224 10.21 Kbp 3211 10.21 Kbp
1.000x 3225 0.92 Gbp 3212 0.92 Gbp
NG based on genome size 1.03 Gbp.
Assembly Metadata
assembly_vgp_standard_2.0/bLagMut1.yaml (view)
species: Lagomus_muta
specimen: bLagMut1
projects:
  - vgp
release_to: S3
data_location: S3
primary: s3://genomeark/species/Lagopus_muta/bLagMut1/assembly_vgp_standard_2.0/bLagMut1.pri.asm.20210815.fasta.gz
haplotigs: s3://genomeark/species/Lagopus_muta/bLagMut1/assembly_vgp_standard_2.0/bLagMut1.alt.asm.20210815.fasta.gz
hic_bam: s3://genomeark/species/Lagopus_muta/bLagMut1/assembly_vgp_standard_2.0/evaluation/LagMut1.pri.asm_pretext/LagMut1.pri.asm.bam
pretext: s3://genomeark/species/Lagopus_muta/bLagMut1/assembly_vgp_standard_2.0/evaluation/LagMut1.pri.asm_pretext/LagMut1.pri.asm.pretext
kmer_spectra_img: s3://genomeark/species/Lagopus_muta/bLagMut1/assembly_vgp_standard_2.0/evaluation/p/Merqury/
pacbio_read_dir: s3://genomeark/species/Lagopus_muta/bLagMut1/genomic_data/
hic_read_dir: s3://genomeark/species/Lagopus_muta/bLagMut1/genomic_data/
rna_seq_read_dir: s3://genomeark/species/Lagopus_muta/bLagMut1/transcriptomic_data/
pacbio_read_type: hifi
hic_kit: dovetail
pipeline:
  - hifiasm (0.15.1-r334)
  - purge_dups (1.2.5)
  - salsa (2.3)
notes:
  No mitogenome has been assembled.
 
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.