Amblyraja radiata

Thorny skate

Included in the VGP.

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


Resource Primary Assembly Alternate Assembly
GenBank sAmbRad1: GCA_010909765.2 sAmbRad1: GCA_010909745.1
ENA sAmbRad1: GCA_010909765.2 sAmbRad1: GCA_010909745.1
UCSC Genome Browser sAmbRad1: GCA_010909765.2 sAmbRad1: GCA_010909745.1

metadata.yaml (view) (edit on github)
species:
  short_name: sAmbRad
  name: Amblyraja radiata
  taxon_id: 386614
  common_name: Thorny skate
  order:
    name: Rajiformes
  family:
    name: Rajidae
  individuals:
    - short_name: sAmbRad1
  genome_size: 2072923533
  genome_size_method:
  project: [ vgp ]
public domain
Raw Data by Technology
Datatype Individual Bases Coverage Bytes Access
PacBio CLR sAmbRad1 265.56 Gbp 128.11x 467.2 GiB
10x sAmbRad1 196.36 Gbp 94.73x 114.7 GiB
Bionano sAmbRad1 N/A 1549.31x 4.9 GiB
Arima sAmbRad1 347.59 Gbp 167.68x 167.9 GiB
Illumina sAmbRad1 233.70 Gbp 112.74x 115.5 GiB
sAmbRad2 127.25 Gbp 61.39x 63.1 GiB
sAmbRad3 127.80 Gbp 61.65x 63.9 GiB
sAmbRad4 121.52 Gbp 58.62x 60.6 GiB
sAmbRad5 158.25 Gbp 76.34x 77.2 GiB
Bases and Coverage are approximate.
Coverage based on genome size 2.07 Gbp.
Last upload on 25 November 2019.
Raw Data by Individual
Individual Datatype Bases Coverage Bytes Access
sAmbRad1 PacBio CLR 265.56 Gbp 128.11x 467.2 GiB
10x 196.36 Gbp 94.73x 114.7 GiB
Bionano N/A 1549.31x 4.9 GiB
Arima 347.59 Gbp 167.68x 167.9 GiB
Illumina 233.70 Gbp 112.74x 115.5 GiB
sAmbRad2 Illumina 127.25 Gbp 61.39x 63.1 GiB
sAmbRad3 Illumina 127.80 Gbp 61.65x 63.9 GiB
sAmbRad4 Illumina 121.52 Gbp 58.62x 60.6 GiB
sAmbRad5 Illumina 158.25 Gbp 76.34x 77.2 GiB
Bases and Coverage are approximate.
Coverage based on genome size 2.07 Gbp.
Last upload on 25 November 2019.
Assemblies
Individual 1 Primary Assembly
Version assembly_curated from 15 December 2020
sAmbRad1.pri.cur.20201215.fasta.gz (687.6 MiB)

Quality: 117.6 errors/Mb (QV=39.30)

Contigs Scaffolds
NG LG Len LG Len
10 31 4.85 Mbp 1 151.57 Mbp
20 81 3.40 Mbp 2 131.32 Mbp
30 151 2.57 Mbp 4 115.64 Mbp
40 243 2.06 Mbp 6 91.02 Mbp
50 357 1.64 Mbp 8 75.33 Mbp
60 497 1.34 Mbp 11 62.87 Mbp
70 675 1.01 Mbp 15 52.89 Mbp
80 917 0.73 Mbp 19 46.75 Mbp
90 1262 495.87 Kbp 23 40.56 Mbp
100 1817 277.84 Kbp 29 33.34 Mbp
1.142x 4710 2.37 Gbp 957 2.56 Gbp
NG based on genome size 2.07 Gbp.
Individual 1 Alternate Assembly
Version assembly_curated from 15 December 2020
sAmbRad1.alt.cur.20201215.fasta.gz (423.3 MiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 1027 149.56 Kbp 1027 149.56 Kbp
20 2698 107.12 Kbp 2698 107.16 Kbp
30 4902 83.52 Kbp 4901 83.52 Kbp
40 7649 68.58 Kbp 7648 68.58 Kbp
50 10975 56.64 Kbp 10973 56.66 Kbp
60 15089 44.17 Kbp 15087 44.17 Kbp
70 21238 19.64 Kbp 21236 19.64 Kbp
80 0 0
90 0 0
100 0 0
0.705x 21995 1.46 Gbp 21992 1.46 Gbp
NG based on genome size 2.07 Gbp.
Individual 1 Mitochondrial Assembly
Version assembly_MT_rockefeller_nanopore from 15 April 2020
sAmbRad1.MT.20200415.fasta.gz (5.0 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.