Gavia stellata

red-throated loon

Included in the VGP.

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


metadata.yaml (view) (edit on github)
species:
  short_name: bGavSte
  name: Gavia stellata
  taxon_id: 37040
  common_name: red-throated loon
  order:
    name: Gaviiformes
  family:
    name: Gaviidae
  individuals:
    - short_name: bGavSte5
      biosample_id: SAMEA9850966
      sex: female
  genome_size: 1398540000
  genome_size_method: GoaT
  project: [ vgp ]
No image
Raw Data by Technology
Datatype Individual Bases Coverage Bytes Access
PacBio HiFi (subreads) bGavSte3 971.55 Gbp 694.69x 1.7 TiB
PacBio HiFi (.fq) bGavSte3 40.98 Gbp 29.30x 29.4 GiB
PacBio HiFi (.bam) bGavSte5 13.50 Gbp 9.65x 7.2 GiB
Arima bGavSte3 151.87 Gbp 108.59x 75.5 GiB
Bases and Coverage are approximate.
Coverage based on genome size 1.40 Gbp.
Last upload on 6 February 2024.
Raw Data by Individual
Individual Datatype Bases Coverage Bytes Access
bGavSte3 PacBio HiFi (subreads) 971.55 Gbp 694.69x 1.7 TiB
PacBio HiFi (.fq) 40.98 Gbp 29.30x 29.4 GiB
Arima 151.87 Gbp 108.59x 75.5 GiB
bGavSte5 PacBio HiFi (.bam) 13.50 Gbp 9.65x 7.2 GiB
Bases and Coverage are approximate.
Coverage based on genome size 1.40 Gbp.
Last upload on 6 February 2024.
Assemblies
Individual 3 Haplotype 1 Assembly
Version assembly_curated from 27 June 2023
bGavSte3.hap1.cur.20230627.fasta.gz (380.9 MiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 4 30.29 Mbp 2 113.82 Mbp
20 10 21.88 Mbp 3 105.09 Mbp
30 17 18.14 Mbp 4 89.71 Mbp
40 26 15.22 Mbp 6 66.80 Mbp
50 36 12.02 Mbp 8 50.56 Mbp
60 49 9.70 Mbp 12 33.66 Mbp
70 68 5.51 Mbp 17 22.27 Mbp
80 105 2.54 Mbp 25 13.79 Mbp
90 312 165.94 Kbp 107 229.14 Kbp
100 3225 12.60 Kbp 2965 12.60 Kbp
1.000x 3225 1.40 Gbp 2965 1.40 Gbp
NG based on genome size 1.40 Gbp.
Individual 3 Haplotype 2 Assembly
Version assembly_curated from 27 June 2023
bGavSte3.hap2.cur.20230627.fasta.gz (372.5 MiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 4 26.91 Mbp 1 133.33 Mbp
20 9 22.60 Mbp 3 105.02 Mbp
30 15 19.36 Mbp 4 89.49 Mbp
40 22 16.63 Mbp 6 65.28 Mbp
50 31 13.77 Mbp 8 50.64 Mbp
60 42 10.60 Mbp 10 41.84 Mbp
70 58 6.69 Mbp 15 25.04 Mbp
80 88 3.02 Mbp 21 18.13 Mbp
90 161 0.95 Mbp 32 6.70 Mbp
100 1434 17.34 Kbp 1185 17.34 Kbp
1.000x 1434 1.32 Gbp 1185 1.32 Gbp
NG based on genome size 1.40 Gbp.
Individual 3 Mitochondrial Assembly
Version assembly_MT_rockefeller from 7 April 2023
bGavSte3.MT.20230407.fasta.gz (5.5 KiB)

Quality: not computed
Assembly Metadata
assembly_vgp_HiC_2.0/bGavSte3_hap1.yml (view)
species: Gavia stellata
specimen: bGavSte3
projects: 
  - vgp
data_location: S3
release_to: S3
haplotype_to_curate: hap1
hap1: s3://genomeark/species/Gavia_stellata/bGavSte3/assembly_vgp_HiC_2.0/bGavSte3.HiC.hap1.20230407.fasta.gz
hap2: s3://genomeark/species/Gavia_stellata/bGavSte3/assembly_vgp_HiC_2.0/bGavSte3.HiC.hap2.20230407.fasta.gz
pretext_hap1: s3://genomeark/species/Gavia_stellata/bGavSte3/assembly_vgp_HiC_2.0/evaluation/hap1/pretext/bGavSte3_hap1__s2_heatmap.pretext
pretext_hap2: s3://genomeark/species/Gavia_stellata/bGavSte3/assembly_vgp_HiC_2.0/evaluation/hap2/pretext/bGavSte3_hap2__s2_heatmap.pretext
kmer_spectra_img: s3://genomeark/species/Gavia_stellata/bGavSte3/assembly_vgp_HiC_2.0/evaluation/merqury/bGavSte3_png/
mito: s3://genomeark/species/Gavia_stellata/bGavSte3/assembly_MT_rockefeller/bGavSte3.MT.20230407.fasta.gz
pacbio_read_dir: s3://genomeark/species/Gavia_stellata/bGavSte3/genomic_data/pacbio_hifi/
pacbio_read_type: hifi
hic_read_dir: s3://genomeark/species/Gavia_stellata/bGavSte3/genomic_data/arima/
pipeline:
  - hifiasm (0.18.8+galaxy1)
  - yahs (1.2a.2+galaxy0)
assembled_by_group: Rockefeller
notes: This was a hifiasm-HiC assembly of bGavSte3, resulting in two complete haplotypes. This individual did not have bionano data. HiC scaffolding was performed with yahs. The HiC prep was Arima kit 2. I am submitting both hap1 & hap2 for dual curation. This is the curation ticket for hap1.
assembly_vgp_HiC_2.0/bGavSte3_hap2.yml (view)
species: Gavia stellata
specimen: bGavSte3
projects: 
  - vgp
data_location: S3
release_to: S3
haplotype_to_curate: hap2
hap1: s3://genomeark/species/Gavia_stellata/bGavSte3/assembly_vgp_HiC_2.0/bGavSte3.HiC.hap1.20230407.fasta.gz
hap2: s3://genomeark/species/Gavia_stellata/bGavSte3/assembly_vgp_HiC_2.0/bGavSte3.HiC.hap2.20230407.fasta.gz
pretext_hap1: s3://genomeark/species/Gavia_stellata/bGavSte3/assembly_vgp_HiC_2.0/evaluation/hap1/pretext/bGavSte3_hap1__s2_heatmap.pretext
pretext_hap2: s3://genomeark/species/Gavia_stellata/bGavSte3/assembly_vgp_HiC_2.0/evaluation/hap2/pretext/bGavSte3_hap2__s2_heatmap.pretext
kmer_spectra_img: s3://genomeark/species/Gavia_stellata/bGavSte3/assembly_vgp_HiC_2.0/evaluation/merqury/bGavSte3_png/
mito: s3://genomeark/species/Gavia_stellata/bGavSte3/assembly_MT_rockefeller/bGavSte3.MT.20230407.fasta.gz
pacbio_read_dir: s3://genomeark/species/Gavia_stellata/bGavSte3/genomic_data/pacbio_hifi/
pacbio_read_type: hifi
hic_read_dir: s3://genomeark/species/Gavia_stellata/bGavSte3/genomic_data/arima/
pipeline:
  - hifiasm (0.18.8+galaxy1)
  - yahs (1.2a.2+galaxy0)
assembled_by_group: Rockefeller
notes: This was a hifiasm-HiC assembly of bGavSte3, resulting in two complete haplotypes. This individual did not have bionano data. HiC scaffolding was performed with yahs. The HiC prep was Arima kit 2. I am submitting both hap1 & hap2 for dual curation. This is the curation ticket for hap2.
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.