Mesoplodon densirostris

Blainville's beaked whale

Included in the VGP.

- S3 File Index -- S3 Interactive Viewer -- NCBI Taxonomy Browser -


Resource Primary Assembly Alternate Assembly
GenBank mMesDen1: GCA_025265405.1 mMesDen1: GCA_025094165.1
ENA mMesDen1: GCA_025265405.1 mMesDen1: GCA_025094165.1
UCSC Genome Browser mMesDen1: GCA_025265405.1 mMesDen1: GCA_025094165.1

metadata.yaml (view) (edit on github)
species:
  name: Mesoplodon densirostris
  individuals:
  - short_name: mMesDen1
  short_name: mMesDen
  taxon_id: 48708
  common_name: Blainville's beaked whale
  genome_size: 3377000000
  genome_size_method: GoAT
  order:
    name: Artiodactyla
  family:
    name: Ziphiidae
  project: [ vgp ]
CC BY-SA 3.0 MatthewGrammatico (Wikimedia)
Raw Data by Technology
Datatype Individual Bases Coverage Bytes Access
PacBio HiFi (subreads) mMesDen1 398.71 Gbp 118.07x 0.9 TiB
PacBio HiFi (.fq) mMesDen1 113.63 Gbp 33.65x 87.8 GiB
PacBio HiFi (.bam) mMesDen1 113.68 Gbp 33.66x 386.0 GiB
Bionano mMesDen1 N/A 214.97x 1.1 GiB
Bases and Coverage are approximate.
Coverage based on genome size 3.38 Gbp.
Last upload on 3 May 2022.
Raw Data by Individual
Individual Datatype Bases Coverage Bytes Access
mMesDen1 PacBio HiFi (subreads) 398.71 Gbp 118.07x 0.9 TiB
PacBio HiFi (.fq) 113.63 Gbp 33.65x 87.8 GiB
PacBio HiFi (.bam) 113.68 Gbp 33.66x 386.0 GiB
Bionano N/A 214.97x 1.1 GiB
Bases and Coverage are approximate.
Coverage based on genome size 3.38 Gbp.
Last upload on 3 May 2022.
Assemblies
Individual 1 Primary Assembly
Version assembly_curated from 30 March 2022
mMesDen1.pri.cur.20220330.fasta.gz (727.4 MiB)

Quality: 0.1 errors/Mb (QV=71.66)

Contigs Scaffolds
NG LG Len LG Len
10 2 107.70 Mbp 1 193.42 Mbp
20 6 75.75 Mbp 3 184.91 Mbp
30 11 61.30 Mbp 5 142.13 Mbp
40 17 48.25 Mbp 7 125.81 Mbp
50 25 40.14 Mbp 10 111.29 Mbp
60 34 31.41 Mbp 14 91.99 Mbp
70 49 13.31 Mbp 17 78.60 Mbp
80 0 0
90 0 0
100 0 0
0.794x 170 2.68 Gbp 73 2.68 Gbp
NG based on genome size 3.38 Gbp.
Individual 1 Alternate Assembly
Version assembly_curated from 30 March 2022
mMesDen1.alt.cur.20220330.fasta.gz (646.0 MiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 72 3.54 Mbp 72 3.54 Mbp
20 192 2.35 Mbp 192 2.35 Mbp
30 362 1.67 Mbp 362 1.67 Mbp
40 604 1.17 Mbp 604 1.17 Mbp
50 958 0.78 Mbp 958 0.78 Mbp
60 1562 392.24 Kbp 1562 392.24 Kbp
70 4652 29.31 Kbp 4651 29.35 Kbp
80 0 0
90 0 0
100 0 0
0.704x 5198 2.38 Gbp 5197 2.38 Gbp
NG based on genome size 3.38 Gbp.
Individual 1 Mitochondrial Assembly
Version assembly_MT_rockefeller from 17 June 2022
mMesDen1.MT.20220617.fasta.gz (4.9 KiB)

Quality: not computed
Assembly Metadata
assembly_vgp_standard_2.0/mMesDen1.yaml (view)
species: Mesoplopdon_densirostris
specimen: mMesDen1
projects:
- vgp
primary:
    s3://genomeark/species/Mesoplodon_densirostris/mMesDen1/assembly_vgp_standard_2.0/mMesDen1.pri.asm.20220215.fasta.gz
haplotigs:
    s3://genomeark/species/Mesoplodon_densirostris/mMesDen1/assembly_vgp_standard_2.0/mMesDen1.alt.asm.20220127.fasta.gz
hic_bam:
    s3://genomeark/species/Mesoplodon_densirostris/mMesDen1/assembly_vgp_standard_2.0/evaluation/pretext/s2/mMesDen1_s2.bam
pretext:
    s3://genomeark/species/Mesoplodon_densirostris/mMesDen1/assembly_vgp_standard_2.0/evaluation/pretext/s2/mMesDen1_heatmap.pretext
kmer_spectra_img:
    s3://genomeark/species/Mesoplodon_densirostris/mMesDen1/assembly_vgp_standard_2..0/evaluation/merqury/p/mMesDen1_png/output_merqury.spectra-cn.fl.png
pipeline:
  - hifiasm (0.16.1+galaxy1)
  - purge_dups (1.2.5+galaxy3)
  - solve (3.7.0+galaxy0)
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.