Porphyrio hochstetteri

South Island takahē

Included in the VGP.

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


Resource Maternal Assembly Paternal Assembly
GenBank bPorHoc1: GCA_020801775.1
ENA bPorHoc1: GCA_020801775.1
UCSC Genome Browser bPorHoc1: GCA_020801775.1

metadata.yaml (view) (edit on github)
species:
  short_name: bPorHoc
  name: Porphyrio hochstetteri
  taxon_id: 439704
  common_name: South Island takahē
  order:
    name: Gruiformes
  family:
    name: Rallidae
  individuals:
    - short_name: bPorHoc1
      provider: Glen Greaves, Lara Urban
      mother: bPorHoc2
      father: bPorHoc3
    - short_name: bPorHoc2
      sex: female
      provider: Glen Greaves, Lara Urban
    - short_name: bPorHoc3
      sex: male
      provider: Glen Greaves, Lara Urban
  genome_size: 1200000000
  genome_size_method:
  project: [ vgp ]
CC BY-NC-SA 2.0 Jake Osborne (flickr)
Raw Data by Technology
Datatype Individual Bases Coverage Bytes Access
PacBio HiFi (subreads) bPorHoc1 773.99 Gbp 644.99x 1.4 TiB
PacBio HiFi (.bam) bPorHoc1 43.98 Gbp 36.65x 36.5 GiB
Bionano bPorHoc1 N/A 407.45x 872.8 MiB
Arima bPorHoc1 123.89 Gbp 103.24x 84.2 GiB
Illumina bPorHoc2 99.86 Gbp 83.22x 47.0 GiB
bPorHoc3 68.15 Gbp 56.79x 32.2 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
bPorHoc1 PacBio HiFi (subreads) 773.99 Gbp 644.99x 1.4 TiB
PacBio HiFi (.bam) 43.98 Gbp 36.65x 36.5 GiB
Bionano N/A 407.45x 872.8 MiB
Arima 123.89 Gbp 103.24x 84.2 GiB
bPorHoc2 Illumina 99.86 Gbp 83.22x 47.0 GiB
bPorHoc3 Illumina 68.15 Gbp 56.79x 32.2 GiB
Bases and Coverage are approximate.
Coverage based on genome size 1.20 Gbp.
Last upload on 3 May 2022.
Assemblies
Individual 1 Merged Trio Assembly
Version assembly_curated from 20 July 2021
bPorHoc1.mat.Z.cur.20210720.fasta.gz (358.2 MiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 3 29.37 Mbp 0 224.11 Mbp
20 8 23.13 Mbp 1 171.06 Mbp
30 13 19.48 Mbp 1 171.06 Mbp
40 20 16.74 Mbp 2 127.87 Mbp
50 28 13.52 Mbp 3 92.51 Mbp
60 37 11.59 Mbp 5 46.77 Mbp
70 50 7.96 Mbp 8 36.67 Mbp
80 68 5.43 Mbp 12 24.25 Mbp
90 100 2.75 Mbp 18 16.64 Mbp
100 178 0.77 Mbp 30 4.96 Mbp
1.054x 501 1.27 Gbp 174 1.27 Gbp
NG based on genome size 1.20 Gbp.
Individual 1 Maternal Assembly
Version assembly_curated from 20 July 2021
bPorHoc1.mat.decon.20210720.fasta.gz (329.1 MiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 3 29.37 Mbp 0 168.54 Mbp
20 8 22.78 Mbp 1 135.46 Mbp
30 14 18.13 Mbp 2 125.85 Mbp
40 20 16.56 Mbp 3 86.48 Mbp
50 29 13.47 Mbp 5 54.21 Mbp
60 38 11.11 Mbp 7 44.49 Mbp
70 52 7.39 Mbp 10 34.45 Mbp
80 73 4.04 Mbp 16 17.57 Mbp
90 121 1.45 Mbp 26 7.59 Mbp
100 0 0
0.978x 445 1.17 Gbp 227 1.18 Gbp
NG based on genome size 1.20 Gbp.
Individual 1 Paternal Assembly
Version assembly_curated from 20 July 2021
bPorHoc1.pat.decon.20210720.fasta.gz (351.6 MiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 3 33.46 Mbp 0 168.78 Mbp
20 7 27.79 Mbp 1 125.97 Mbp
30 12 21.76 Mbp 2 92.69 Mbp
40 18 17.86 Mbp 4 77.82 Mbp
50 26 13.97 Mbp 5 71.52 Mbp
60 35 12.19 Mbp 7 46.84 Mbp
70 47 7.83 Mbp 10 36.80 Mbp
80 66 5.24 Mbp 14 23.96 Mbp
90 97 2.72 Mbp 20 16.65 Mbp
100 195 0.55 Mbp 35 2.44 Mbp
1.029x 416 1.23 Gbp 178 1.25 Gbp
NG based on genome size 1.20 Gbp.
Individual 1 Mitochondrial Assembly
Version assembly_vgp_standard_2.0 from 4 June 2021
bPorHoc1.MT.20210604.fasta.gz (5.4 KiB)

Quality: not computed
Assembly Metadata
bPorHoc1_metadata.yml (view)
samples:
- biomaterial_provider: "Burwood Takah\u0113 Centre (New Zealand)"
  bioproject_accession: PRJNA516733
  birth_date: ''
  birth_location: ''
  breed: ''
  collected_by: Glen Greaves
  collection_date: 02/13/2020
  common_name: South_Island_takahe
  description: Offspring- "Kohika"
  dev_stage: juvenile
  geo_loc_name: Te Anau, New Zealand
  isolate: bPorHoc1
  lat_lon: 45.41 S, 167.71 E
  organism: Porphyrio hochstetteri
  sex: female
  specimen_voucher: ''
  store_cond: -80C
  taxon_Id: '439704'
  tissue: Whole blood
  treatment: 99% ethanol, frozen
  tube_id: bPorHoc1
bPorHoc2_metadata.yml (view)
samples:
- biomaterial_provider: "Burwood Takah\u0113 Centre (New Zealand)"
  bioproject_accession: PRJNA516733
  birth_date: ''
  birth_location: ''
  breed: ''
  collected_by: Glen Greaves
  collection_date: 02/13/2020
  common_name: South_Island_takahe
  description: mother of bPorHoc1
  dev_stage: adult
  geo_loc_name: Te Anau, New Zealand
  isolate: bPorHoc2
  lat_lon: 45.41 S, 167.71 E
  organism: Porphyrio hochstetteri
  sex: female
  specimen_voucher: ''
  store_cond: -80C
  taxon_Id: '439704'
  tissue: Whole blood
  treatment: 99% ethanol, frozen
  tube_id: bPorHoc2
bPorHoc3_metadata.yml (view)
samples:
- biomaterial_provider: "Burwood Takah\u0113 Centre (New Zealand)"
  bioproject_accession: PRJNA516733
  birth_date: ''
  birth_location: ''
  breed: ''
  collected_by: Glen Greaves
  collection_date: 02/13/2020
  common_name: South_Island_takahe
  description: father of bPorHoc1
  dev_stage: adult
  geo_loc_name: Te Anau, New Zealand
  isolate: bPorHoc3
  lat_lon: 45.41 S, 167.71 E
  organism: Porphyrio hochstetteri
  sex: male
  specimen_voucher: ''
  store_cond: -80C
  taxon_Id: '439704'
  tissue: Whole blood
  treatment: 99% ethanol, frozen
  tube_id: bPorHoc3
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.