Hypanus sabinus

Atlantic stingray

Included in the VGP.

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


Resource Primary Assembly Alternate Assembly
GenBank sHypSab1: GCA_030144785.1 sHypSab1: GCA_030144855.1
ENA sHypSab1: GCA_030144785.1 sHypSab1: GCA_030144855.1
UCSC Genome Browser sHypSab1: GCA_030144785.1 sHypSab1: GCA_030144855.1

metadata.yaml (view) (edit on github)
species:
  name: Hypanus sabinus
  individuals:
  - short_name: sHypSab1
  short_name: sHypSab
  taxon_id: 79690
  common_name: Atlantic stingray
  genome_size: 4108000000
  genome_size_method: GoAT
  order:
    name: Myliobatiformes
  family:
    name: Dasyatidae
  project: [ vgp ]
CC BY-SA 4.0 Coughdrop12 (Wikimedia)
Raw Data by Technology
Datatype Individual Bases Coverage Bytes Access
PacBio HiFi (.fq) sHypSab1 140.51 Gbp 34.20x 105.1 GiB
Arima sHypSab1 319.58 Gbp 77.79x 161.8 GiB
Bases and Coverage are approximate.
Coverage based on genome size 4.11 Gbp.
Last upload on 27 May 2022.
Raw Data by Individual
Individual Datatype Bases Coverage Bytes Access
sHypSab1 PacBio HiFi (.fq) 140.51 Gbp 34.20x 105.1 GiB
Arima 319.58 Gbp 77.79x 161.8 GiB
Bases and Coverage are approximate.
Coverage based on genome size 4.11 Gbp.
Last upload on 27 May 2022.
Assemblies
Individual 1 Haplotype 1 Assembly
Version assembly_curated from 25 April 2023
sHypSab1.hap1.cur.20230425.fasta.gz (1.1 GiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 19 15.70 Mbp 2 212.30 Mbp
20 51 10.73 Mbp 5 187.19 Mbp
30 96 8.06 Mbp 7 182.41 Mbp
40 158 5.77 Mbp 9 169.66 Mbp
50 241 4.17 Mbp 12 112.26 Mbp
60 361 2.85 Mbp 16 90.80 Mbp
70 544 1.79 Mbp 21 70.26 Mbp
80 847 0.99 Mbp 28 46.44 Mbp
90 1527 372.37 Kbp 225 0.57 Mbp
100 0 0
0.982x 4617 4.03 Gbp 2978 4.03 Gbp
NG based on genome size 4.11 Gbp.
Individual 1 Haplotype 2 Assembly
Version assembly_curated from 25 April 2023
sHypSab1.hap2.cur.20230425.fasta.gz (1.0 GiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 17 17.98 Mbp 2 210.74 Mbp
20 46 11.72 Mbp 5 186.50 Mbp
30 88 7.85 Mbp 7 177.59 Mbp
40 151 5.58 Mbp 9 166.19 Mbp
50 238 3.87 Mbp 12 112.88 Mbp
60 368 2.56 Mbp 16 91.03 Mbp
70 568 1.60 Mbp 21 69.65 Mbp
80 977 0.61 Mbp 29 40.02 Mbp
90 0 0
100 0 0
0.884x 3040 3.63 Gbp 1409 3.63 Gbp
NG based on genome size 4.11 Gbp.
Assembly Metadata
assembly_vgp_HiC_2.0/sHypSab1.yaml (view)
species: Hypanus sabinus
specimen: sHypSab1
projects:
  - vgp
hap1: s3://genomeark/species/species/Hypanus_sabinus/sHypSab1/assembly_vgp_HiC_2.0/sHypSab1.HiC.hap1.20220617.fasta.gz
hap2: s3://genomeark/species/species/Hypanus_sabinus/sHypSab1/assembly_vgp_HiC_2.0/sHypSab1.HiC.hap2.20220617.fasta.gz
hap1_pretext: s3://genomeark/species/Hypanus_sabinus/sHypSab1/assembly_vgp_HiC_2.0/evaluation/hap1/pretext/sHypSab1_hap1__s2_heatmap.pretext
hap2_pretext: s3://genomeark/species/Hypanus_sabinus/sHypSab1/assembly_vgp_HiC_2.0/evaluation/hap2/pretext/sHypSab1_hap2__s2_heatmap.pretext
kmer_spectra_img: s3://genomeark/species/Hypanus_sabinus/sHypSab1/assembly_vgp_HiC_2.0/evaluation/merqury/sHypSab1_png/
pacbio_read_dir: s3://genomeark/species/Hypanus_sabinus/sHypSab1/genomic_data/pacbio_hifi/
pacbio_read_type: hifi
hic_read_dir: s3://genomeark/species/Hypanus_sabinus/sHypSab1/genomic_data/arima/
pipeline:
  - hifiasm (0.16.1+galaxy2)
  - yahs (1.2a+galaxy1)
assembled_by_group: Rockefeller
notes: This individual did not have bionano data. This assembly was done with Hifiasm-HiC mode, resulting in two complete haplotypes. Kmer spectra probably indicate a heterogametic specimen, likely will need fishing for the sex chromosomes between the two haplotypes, hence submitting both haplotypes.  
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.