Coturnix chinensis

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Raw Data by Technology
Datatype Individual Bases Coverage Bytes Access
PacBio HiFi (.fq) bCotChi1 50.67 Gbp N/A 41.9 GiB
Arima bCotChi1 120.36 Gbp N/A 58.8 GiB
Bases and Coverage are approximate.
Coverage based on genome size .
Last upload on 17 May 2023.
Raw Data by Individual
Individual Datatype Bases Coverage Bytes Access
bCotChi1 PacBio HiFi (.fq) 50.67 Gbp N/A 41.9 GiB
Arima 120.36 Gbp N/A 58.8 GiB
Bases and Coverage are approximate.
Coverage based on genome size .
Last upload on 17 May 2023.
Assemblies
Individual 1 Haplotype 1 Assembly
Version assembly_vgp_HiC_2.0 from 3 October 2023
bCotChi1.HiC.hap1.20231003.fasta.gz (282.7 MiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 3 24.53 Mbp 1 183.56 Mbp
20 8 15.98 Mbp 2 140.50 Mbp
30 15 11.40 Mbp 2 140.50 Mbp
40 25 8.69 Mbp 3 104.65 Mbp
50 37 6.81 Mbp 4 85.71 Mbp
60 53 5.44 Mbp 6 56.51 Mbp
70 75 3.72 Mbp 8 34.89 Mbp
80 109 2.14 Mbp 11 22.16 Mbp
90 171 1.12 Mbp 17 13.10 Mbp
100 803 12.32 Kbp 502 12.32 Kbp
1.000x 803 0.98 Gbp 502 0.98 Gbp
NG based on genome size .
Individual 1 Haplotype 2 Assembly
Version assembly_vgp_HiC_2.0 from 3 October 2023
bCotChi1.HiC.hap2.20231003.fasta.gz (280.7 MiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 3 24.41 Mbp 1 183.08 Mbp
20 8 17.68 Mbp 2 140.71 Mbp
30 14 12.96 Mbp 2 140.71 Mbp
40 22 10.63 Mbp 3 105.06 Mbp
50 33 7.82 Mbp 4 86.36 Mbp
60 48 6.02 Mbp 5 69.05 Mbp
70 66 3.98 Mbp 7 37.71 Mbp
80 97 2.61 Mbp 10 28.13 Mbp
90 151 1.22 Mbp 16 13.64 Mbp
100 534 17.30 Kbp 232 17.30 Kbp
1.000x 534 0.97 Gbp 232 0.97 Gbp
NG based on genome size .
Individual 1 Mitochondrial Assembly
Version assembly_MT_rockefeller from 5 January 2024
bCotChi1.MT.20240105.fasta.gz (5.4 KiB)

Quality: not computed
Assembly Metadata
assembly_vgp_HiC_2.0/bCotChi1_hap1.yml (view)
species: Coturnix chinensis
specimen: bCotChi1
projects: 
  - vgp
assembled_by_group: Rockefeller
data_location: S3
release_to: S3
haplotype_to_curate: hap1
hap1: s3://genomeark/species/Coturnix_chinensis/bCotChi1/assembly_vgp_HiC_2.0/bCotChi1.HiC.hap1.20231003.fasta.gz
hap2: s3://genomeark/species/Coturnix_chinensis/bCotChi1/assembly_vgp_HiC_2.0/bCotChi1.HiC.hap2.20231003.fasta.gz
pretext_hap1: s3://genomeark/species/Coturnix_chinensis/bCotChi1/assembly_vgp_HiC_2.0/evaluation/hap1/pretext/bCotChi1_hap1_s2.pretext
pretext_hap2: s3://genomeark/species/Coturnix_chinensis/bCotChi1/assembly_vgp_HiC_2.0/evaluation/hap2/pretext/bCotChi1_hap2_s2.pretext
kmer_spectra_img: s3://genomeark/species/Coturnix_chinensis/bCotChi1/assembly_vgp_HiC_2.0/evaluation/merqury/bCotChi1_png/
pacbio_read_dir: s3://genomeark/species/Coturnix_chinensis/bCotChi1/genomic_data/pacbio_hifi/
pacbio_read_type: hifi
hic_read_dir: s3://genomeark/species/Coturnix_chinensis/bCotChi1/genomic_data/arima/
pipeline: 
  - hifiasm (0.16.1+galaxy4)
  - yahs (1.2a.2+galaxy1)
notes: This was a Hifiasm-HiC assembly of bCotChi1, resulting in two complete haplotypes. HiC scaffolding was performed with YaHS.  The HiC prep kit used was Arima.  
assembly_vgp_HiC_2.0/bCotChi1_hap2.yml (view)
species: Coturnix chinensis
specimen: bCotChi1
projects: 
  - vgp
assembled_by_group: Rockefeller
data_location: S3
release_to: S3
haplotype_to_curate: hap2
hap1: s3://genomeark/species/Coturnix_chinensis/bCotChi1/assembly_vgp_HiC_2.0/bCotChi1.HiC.hap1.20231003.fasta.gz
hap2: s3://genomeark/species/Coturnix_chinensis/bCotChi1/assembly_vgp_HiC_2.0/bCotChi1.HiC.hap2.20231003.fasta.gz
pretext_hap1: s3://genomeark/species/Coturnix_chinensis/bCotChi1/assembly_vgp_HiC_2.0/evaluation/hap1/pretext/bCotChi1_hap1_s2.pretext
pretext_hap2: s3://genomeark/species/Coturnix_chinensis/bCotChi1/assembly_vgp_HiC_2.0/evaluation/hap2/pretext/bCotChi1_hap2_s2.pretext
kmer_spectra_img: s3://genomeark/species/Coturnix_chinensis/bCotChi1/assembly_vgp_HiC_2.0/evaluation/merqury/bCotChi1_png/
pacbio_read_dir: s3://genomeark/species/Coturnix_chinensis/bCotChi1/genomic_data/pacbio_hifi/
pacbio_read_type: hifi
hic_read_dir: s3://genomeark/species/Coturnix_chinensis/bCotChi1/genomic_data/arima/
pipeline: 
  - hifiasm (0.16.1+galaxy4)
  - yahs (1.2a.2+galaxy1)
notes: This was a Hifiasm-HiC assembly of bCotChi1, resulting in two complete haplotypes. HiC scaffolding was performed with YaHS.  The HiC prep kit used was Arima. 
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.