Amazona ochrocephala

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CC BY 2.0 Peter Tan (Wikimedia)
Raw Data by Technology
Datatype Individual Bases Coverage Bytes Access
PacBio HiFi (subreads) bAmaOch1 1350.77 Gbp N/A 2.3 TiB
PacBio HiFi (.fq) bAmaOch1 50.97 Gbp N/A 42.7 GiB
PacBio HiFi (.bam) bAmaOch1 163.04 Gbp N/A 580.7 GiB
Arima bAmaOch1 77.08 Gbp N/A 40.2 GiB
Bases and Coverage are approximate.
Coverage based on genome size .
Last upload on 11 June 2024.
Raw Data by Individual
Individual Datatype Bases Coverage Bytes Access
bAmaOch1 PacBio HiFi (subreads) 1350.77 Gbp N/A 2.3 TiB
PacBio HiFi (.fq) 50.97 Gbp N/A 42.7 GiB
PacBio HiFi (.bam) 163.04 Gbp N/A 580.7 GiB
Arima 77.08 Gbp N/A 40.2 GiB
Bases and Coverage are approximate.
Coverage based on genome size .
Last upload on 11 June 2024.
Assemblies
Individual 1 Haplotype 1 Assembly
Version assembly_vgp_HiC_2.0 from 10 July 2023
bAmaOch1.HiC.hap1.20230710.fasta.gz (328.7 MiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 3 42.41 Mbp 1 137.84 Mbp
20 6 28.39 Mbp 2 132.31 Mbp
30 11 24.54 Mbp 3 125.87 Mbp
40 16 23.11 Mbp 4 93.40 Mbp
50 22 17.62 Mbp 6 86.17 Mbp
60 29 13.61 Mbp 7 74.04 Mbp
70 39 11.45 Mbp 10 32.07 Mbp
80 53 6.89 Mbp 15 17.62 Mbp
90 114 0.65 Mbp 45 0.72 Mbp
100 1803 11.17 Kbp 1684 11.17 Kbp
1.000x 1803 1.21 Gbp 1684 1.21 Gbp
NG based on genome size .
Individual 1 Haplotype 2 Assembly
Version assembly_vgp_HiC_2.0 from 10 July 2023
bAmaOch1.HiC.hap2.20230710.fasta.gz (381.8 MiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 5 28.38 Mbp 2 133.33 Mbp
20 10 24.95 Mbp 3 125.96 Mbp
30 17 22.66 Mbp 4 94.58 Mbp
40 25 17.63 Mbp 6 85.98 Mbp
50 35 12.75 Mbp 8 71.34 Mbp
60 50 7.73 Mbp 11 40.65 Mbp
70 74 4.22 Mbp 16 21.19 Mbp
80 137 1.26 Mbp 35 2.26 Mbp
90 570 170.81 Kbp 435 174.01 Kbp
100 2669 12.66 Kbp 2508 12.66 Kbp
1.000x 2669 1.51 Gbp 2508 1.51 Gbp
NG based on genome size .
Individual 1 Mitochondrial Assembly
Version assembly_MT_rockefeller from 10 July 2023
bAmaOch1.MT.20230710.fasta.gz (5.7 KiB)

Quality: not computed
Assembly Metadata
assembly_vgp_HiC_2.0/bAmaOch1.yml (view)
species: Amazona ochrocephala
specimen: bAmaOch1
projects: 
  - vgp
hap1: s3://genomeark/species/Amazona_ochrocephala/bAmaOch1/assembly_vgp_HiC_2.0/bAmaOch1.HiC.hap1.20230710.fasta.gz
hap2: s3://genomeark/species/Amazona_ochrocephala/bAmaOch1/assembly_vgp_HiC_2.0/bAmaOch1.HiC.hap2.20230710.fasta.gz
pretext_hap1: s3://genomeark/species/Amazona_ochrocephala/bAmaOch1/assembly_vgp_HiC_2.0/evaluation/hap1/pretext/bAmaOch1_hap1__s2_heatmap.pretext
pretext_hap2: s3://genomeark/species/Amazona_ochrocephala/bAmaOch1/assembly_vgp_HiC_2.0/evaluation/hap2/pretext/bAmaOch1_hap2__s2_heatmap.pretext
kmer_spectra_img: s3://genomeark/species/Amazona_ochrocephala/bAmaOch1/assembly_vgp_HiC_2.0/evaluation/merqury/bAmaOch1_png/
mito: s3://genomeark/species/Amazona_ochrocephala/bAmaOch1/assembly_MT_rockefeller/bAmaOch1.MT.20230710.fasta.gz
pipeline:
  - hifiasm (0.19.3+galaxy0)
  - yahs (1.2a.2+galaxy1)
assembled_by_group: Rockefeller
notes: This was a hifiasm-HiC assembly of bAmaOch1, resulting in two complete haplotypes. This individual did not bionano data. HiC scaffolding was performed with yahs. The HiC prep was Arima kit 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.