Phocoena phocoena

harbor porpoise

Included in the VGP.

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


metadata.yaml (view) (edit on github)
species:
  short_name: mPhoPho
  name: Phocoena phocoena
  taxon_id: 9742
  common_name: harbor porpoise
  order:
    name: Cetacea
  family:
    name: Phocoenidae
  individuals:
    - short_name: mPhoPho1
      biosample_id: SAMEA111380536
      sex: female
  genome_size: 3217620000
  genome_size_method: GoaT
  project: [ vgp ]
No image
Raw Data by Technology
Datatype Individual Bases Coverage Bytes Access
PacBio HiFi (.bam) mPhoPho1 58.02 Gbp 18.03x 27.0 GiB
Arima mPhoPho1 446.90 Gbp 138.89x 135.0 GiB
Bases and Coverage are approximate.
Coverage based on genome size 3.22 Gbp.
Last upload on 19 December 2023.
Raw Data by Individual
Individual Datatype Bases Coverage Bytes Access
mPhoPho1 PacBio HiFi (.bam) 58.02 Gbp 18.03x 27.0 GiB
Arima 446.90 Gbp 138.89x 135.0 GiB
Bases and Coverage are approximate.
Coverage based on genome size 3.22 Gbp.
Last upload on 19 December 2023.
Assemblies
Individual 1 Primary Assembly
Version assembly_curated from 26 January 2024
mPhoPho1.pri.cur.20240126.fasta.gz (708.8 MiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 32 8.76 Mbp 2 177.80 Mbp
20 77 6.30 Mbp 4 146.74 Mbp
30 137 4.65 Mbp 7 115.56 Mbp
40 216 3.67 Mbp 9 110.19 Mbp
50 318 2.68 Mbp 12 102.34 Mbp
60 461 1.89 Mbp 16 87.82 Mbp
70 685 1.09 Mbp 20 60.50 Mbp
80 0 0
90 0 0
100 0 0
0.781x 1406 2.51 Gbp 440 2.51 Gbp
NG based on genome size 3.22 Gbp.
Individual 1 Alternate Assembly
Version assembly_curated from 26 January 2024
mPhoPho1.alt.cur.20240126.fasta.gz (735.3 MiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 100 2.41 Mbp 100 2.41 Mbp
20 256 1.80 Mbp 256 1.80 Mbp
30 459 1.39 Mbp 459 1.39 Mbp
40 721 1.10 Mbp 721 1.10 Mbp
50 1060 0.82 Mbp 1060 0.82 Mbp
60 1527 0.57 Mbp 1527 0.57 Mbp
70 2261 327.73 Kbp 2261 327.73 Kbp
80 4142 71.92 Kbp 4142 71.92 Kbp
90 0 0
100 0 0
0.831x 7636 2.67 Gbp 7636 2.67 Gbp
NG based on genome size 3.22 Gbp.
Individual 1 Mitochondrial Assembly
Version assembly_MT_cambridge from 22 December 2023
mPhoPho1.MT.20231222.fasta.gz (5.2 KiB)

Quality: not computed
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.