Pangasianodon hypophthalmus

Iridescent shark

Included in the VGP.

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


Resource Primary Assembly Alternate Assembly
GenBank fPanHyp1: GCA_027358585.1 fPanHyp1: GCA_027382375.1
ENA fPanHyp1: GCA_027358585.1 fPanHyp1: GCA_027382375.1
UCSC Genome Browser fPanHyp1: GCA_027358585.1 fPanHyp1: GCA_027382375.1

metadata.yaml (view) (edit on github)
species:
  short_name: fPanHyp
  name: Pangasianodon hypophthalmus 
  taxon_id: 310915
  common_name: Iridescent shark
  order:
    name: Siluriformes
  family:
    name: Pangasiidae
  individuals:
    - short_name: fPanHyp1
  project: [ vgp ]
Raw Data by Technology
Datatype Individual Bases Coverage Bytes Access
PacBio HiFi (subreads) fPanHyp1 315.56 Gbp 412.51x 565.7 GiB
PacBio HiFi (.bam) fPanHyp1 18.28 Gbp 23.90x 12.3 GiB
Bionano fPanHyp1 N/A 1428.57x 1.6 GiB
Arima fPanHyp1 101.77 Gbp 133.04x 45.0 GiB
Bases and Coverage are approximate.
Coverage based on genome size 0.76 Gbp.
Last upload on 3 May 2022.
Raw Data by Individual
Individual Datatype Bases Coverage Bytes Access
fPanHyp1 PacBio HiFi (subreads) 315.56 Gbp 412.51x 565.7 GiB
PacBio HiFi (.bam) 18.28 Gbp 23.90x 12.3 GiB
Bionano N/A 1428.57x 1.6 GiB
Arima 101.77 Gbp 133.04x 45.0 GiB
Bases and Coverage are approximate.
Coverage based on genome size 0.76 Gbp.
Last upload on 3 May 2022.
Assemblies
Individual 1 Primary Assembly
Version assembly_curated from 9 December 2021
fPanHyp1.pri.cur.20211209.fasta.gz (217.1 MiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 3 22.03 Mbp 2 34.65 Mbp
20 6 19.51 Mbp 4 32.69 Mbp
30 10 16.91 Mbp 6 30.57 Mbp
40 15 14.05 Mbp 9 29.69 Mbp
50 21 13.01 Mbp 12 26.13 Mbp
60 27 10.40 Mbp 15 25.66 Mbp
70 36 6.87 Mbp 18 22.08 Mbp
80 50 4.56 Mbp 21 21.07 Mbp
90 75 1.78 Mbp 25 19.91 Mbp
100 293 282 bp 57 282 bp
1.000x 294 0.76 Gbp 58 0.76 Gbp
NG based on genome size 0.76 Gbp.
Individual 1 Alternate Assembly
Version assembly_curated from 9 December 2021
fPanHyp1.alt.cur.20211209.fasta.gz (211.4 MiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 52 1.06 Mbp 52 1.06 Mbp
20 130 0.84 Mbp 130 0.84 Mbp
30 229 0.67 Mbp 229 0.67 Mbp
40 348 0.56 Mbp 348 0.56 Mbp
50 495 449.89 Kbp 495 449.89 Kbp
60 679 359.14 Kbp 679 359.14 Kbp
70 914 276.44 Kbp 914 276.44 Kbp
80 1233 191.84 Kbp 1233 191.89 Kbp
90 1726 113.74 Kbp 1726 113.74 Kbp
100 3274 7.77 Kbp 3273 9.64 Kbp
1.000x 3275 0.74 Gbp 3274 0.74 Gbp
NG based on genome size 0.76 Gbp.
Individual 1 Mitochondrial Assembly
Version assembly_MT_rockefeller from 13 December 2022
fPanHyp1.MT.20221213.fasta.gz (5.0 KiB)

Quality: not computed
Assembly Metadata
fPanHyp1.yaml (view)
species: Pangasianodon_hypophthalmus
specimen: fPanHyp1
projects:
  - vgp
primary: s3://genomeark/species/Pangasianodon_hypophthalmus/fPanHyp1/assembly_vgp_standard_2.1/
haplotigs: s3://genomeark/species/Pangasianodon_hypophthalmus/fPanHyp1/assembly_vgp_standard_2.1/
release_to: S3
data_location: S3
pacbio_read_dir: s3://genomeark/species/Pangasianodon_hypophthalmus/fPanHyp1/pacbio/
hic_read_dir: s3://genomeark/species/Pangasianodon_hypophthalmus/fPanHyp1/arima/
hic_kit: Arima2
pipeline:
  - hifiasm (0.15.3)
  - purge_dups (1.2.3)
  - bionano_solve (Solve3.6.1_11162020)
  - salsa (v2.2)
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.