Corvus hawaiiensis

hawaiian crow

Included in the VGP.

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


Resource Primary Assembly Alternate Assembly
GenBank bCorHaw1: GCA_020740725.1 bCorHaw1: GCA_020740675.1
ENA bCorHaw1: GCA_020740725.1 bCorHaw1: GCA_020740675.1
UCSC Genome Browser bCorHaw1: GCA_020740725.1 bCorHaw1: GCA_020740675.1

metadata.yaml (view) (edit on github)
species:
  short_name: bCorHaw
  name: Corvus hawaiiensis
  taxon_id: 134902
  common_name: hawaiian crow
  order:
    name: Passeriformes
  family:
    name: Corvidae
  individuals:
    - short_name: bCorHaw1
      sex: female
      provider: Jolene Sutton, Stefanie Großer
  genome_size: 1200000000
  genome_size_method:
  project: [ vgp ]
CC BY-NC 2.0 USFWS - Pacific Region (flickr)
Raw Data by Technology
Datatype Individual Bases Coverage Bytes Access
PacBio HiFi (subreads) bCorHaw1 758.04 Gbp 631.70x 1.3 TiB
PacBio HiFi (.fq) bCorHaw1 18.40 Gbp 15.33x 17.0 GiB
PacBio HiFi (.bam) bCorHaw1 34.66 Gbp 28.88x 29.6 GiB
Bionano bCorHaw1 N/A 423.18x 893.3 MiB
Arima bCorHaw1 86.80 Gbp 72.33x 58.2 GiB
Bases and Coverage are approximate.
Coverage based on genome size 1.20 Gbp.
Last upload on 3 May 2022.
Raw Data by Individual
Individual Datatype Bases Coverage Bytes Access
bCorHaw1 PacBio HiFi (subreads) 758.04 Gbp 631.70x 1.3 TiB
PacBio HiFi (.fq) 18.40 Gbp 15.33x 17.0 GiB
PacBio HiFi (.bam) 34.66 Gbp 28.88x 29.6 GiB
Bionano N/A 423.18x 893.3 MiB
Arima 86.80 Gbp 72.33x 58.2 GiB
Bases and Coverage are approximate.
Coverage based on genome size 1.20 Gbp.
Last upload on 3 May 2022.
Assemblies
Individual 1 Primary Assembly
Version assembly_curated from 20 September 2021
bCorHaw1.pri.cur.20210920.fasta.gz (322.6 MiB)

Quality: 57.3 errors/Mb (QV=42.42)

Contigs Scaffolds
NG LG Len LG Len
10 1 68.42 Mbp 0 123.45 Mbp
20 3 48.06 Mbp 1 121.53 Mbp
30 6 35.05 Mbp 3 80.11 Mbp
40 10 24.60 Mbp 4 79.83 Mbp
50 15 21.25 Mbp 6 66.14 Mbp
60 23 12.49 Mbp 8 40.98 Mbp
70 34 8.83 Mbp 12 23.99 Mbp
80 51 5.63 Mbp 17 21.09 Mbp
90 95 1.55 Mbp 25 8.70 Mbp
100 0 0
0.958x 481 1.15 Gbp 187 1.15 Gbp
NG based on genome size 1.20 Gbp.
Individual 1 Alternate Assembly
Version assembly_curated from 20 September 2021
bCorHaw1.alt.cur.20210920.fasta.gz (178.8 MiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 66 1.27 Mbp 66 1.27 Mbp
20 189 0.79 Mbp 189 0.79 Mbp
30 383 488.30 Kbp 383 488.30 Kbp
40 722 256.24 Kbp 722 256.24 Kbp
50 1935 43.54 Kbp 1935 43.54 Kbp
60 0 0
70 0 0
80 0 0
90 0 0
100 0 0
0.524x 2762 0.63 Gbp 2762 0.63 Gbp
NG based on genome size 1.20 Gbp.
Assembly Metadata
assembly_vgp_standard_2.0/bCorHaw1.yaml (view)
species: Corvus_hawaiiensis
specimen: bCorHaw1
projects:
  - vgp
primary: s3://genomeark/species/Corvus_hawaiiensis/bCorHaw1/assembly_vgp_standard_2.0/bCorHaw1.pri.asm.20212907.fasta
haplotigs: s3://genomeark/species/Corvus_hawaiiensis/bCorHaw1/assembly_vgp_standard_2.0/bCorHaw1.alt.asm.20212707.fasta
pipeline:
  - hifiasm (0.15.4+galaxy)
  - purge_dups (1.2.5+galaxy3)
  - bionano_solve (3.6.1+galaxy2)
  - salsa (2.3+galaxy0)
bCorHaw1_metadata.yml (view)
samples:
- Sample Source: University of Hawaii
  VGP_Id: bCorHaw1
  birth_date: 07/05/2018
  collected_by: Bryce Masuda
  collection_date: 08/08/2020
  common_name: hawaiian crow
  description: "Jolene Sutton (U. Hawai'i), Bruce Robertson and Stefanie Gro\xDFer\
    \ (U. Otago) "
  dev_stage: adult
  geo_loc_name: Hawai'i, USA
  individual_id: ''
  lat_lon: 21.297467,-157.818261
  scientific_name: Corvus hawaiiensis
  sex: female
  store_cond: -80C
  taxon_Id: '134902'
  tissue: Blood
  treatment: 99% ethanol
  tube_id: bCorHaw1.BL1,bCorHaw1.BL2
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.