Gallus gallus

chicken

Included in the VGP.

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


Resource Primary Assembly Alternate Assembly
GenBank bGalGal4: GCA_027557775.1 bGalGal5: GCA_027408225.1 bGalGal4: GCA_027408255.1 bGalGal5: GCA_027408205.1
ENA bGalGal4: GCA_027557775.1 bGalGal5: GCA_027408225.1 bGalGal4: GCA_027408255.1 bGalGal5: GCA_027408205.1
UCSC Genome Browser bGalGal4: GCA_027557775.1 bGalGal5: GCA_027408225.1 bGalGal4: GCA_027408255.1 bGalGal5: GCA_027408205.1

Resource Maternal Assembly Paternal Assembly
GenBank bGalGal1: GCA_016699485.1 bGalGal1: GCA_016700215.2
ENA bGalGal1: GCA_016699485.1 bGalGal1: GCA_016700215.2
UCSC Genome Browser bGalGal1: GCA_016699485.1 bGalGal1: GCA_016700215.2

metadata.yaml (view) (edit on github)
species:
  common_name: chicken
  family:
    name: Phasianidae
  genome_size: 1210000000
  genome_size_method: null
  name: Gallus gallus
  order:
    name: Galliformes
  short_name: bGalGal
  taxon_id: 9031
  individuals:
  - short_name: bGalGal1
    mother: bGalGal2
    father: bGalGal3
    sex: female
    provider: Nick Anthony, Wesley Warren
    description: >
        Broiler x Leghorn cross;
  - short_name: bGalGal2
    sex: female
    description: >
        Broiler breed;
    provider: Nick Anthony, Wesley Warren
  - short_name: bGalGal3
    sex: male
    description: >
        Leghorn breed;
    provider: Nick Anthony, Wesley Warren
  - short_name: bGalGal4
    sex: female
    provider: Joan Tarradas, Antton Alberdi
    description: >
        Broiler Ross breed;
  - short_name: bGalGal5
    provider: Joan Tarradas, Antton Alberdi
    sex: female
    description: >
        Broiler Cobb breed;
  project: [ vgp ]
(pixabay)
Raw Data by Technology
Datatype Individual Bases Coverage Bytes Access
PacBio CLR bGalGal1 123.49 Gbp 102.06x 213.3 GiB
PacBio HiFi (subreads) bGalGal1 1587.32 Gbp 1311.84x 2.7 TiB
bGalGal4 803.98 Gbp 664.44x 1.4 TiB
bGalGal5 733.80 Gbp 606.45x 1.3 TiB
PacBio HiFi (.fq, Q≥20) bGalGal5 0.00x 33.8 GiB
PacBio HiFi (.fq) bGalGal1 92.89 Gbp 76.77x 79.4 GiB
PacBio HiFi (.bam) bGalGal1 261.07 Gbp 215.76x 0.9 TiB
bGalGal4 39.38 Gbp 32.55x 33.7 GiB
Oxford Nanopore Simplex bGalGal1 191.42 Gbp 158.20x 160.4 GiB
10x bGalGal1 95.77 Gbp 79.15x 52.8 GiB
bGalGal4 78.41 Gbp 64.80x 39.1 GiB
bGalGal5 104.31 Gbp 86.21x 51.6 GiB
Bionano bGalGal1 N/A 456.16x 1.0 GiB
bGalGal4 N/A 319.58x 802.4 MiB
bGalGal5 N/A 459.32x 0.9 GiB
Arima bGalGal1 106.22 Gbp 87.78x 63.1 GiB
bGalGal2 100.61 Gbp 83.15x 63.1 GiB
bGalGal3 102.19 Gbp 84.45x 63.0 GiB
bGalGal4 79.34 Gbp 65.57x 52.5 GiB
bGalGal5 147.73 Gbp 122.09x 89.6 GiB
Illumina bGalGal2 103.18 Gbp 85.27x 51.7 GiB
bGalGal3 116.18 Gbp 96.02x 58.0 GiB
Bases and Coverage are approximate.
Coverage based on genome size 1.21 Gbp.
Last upload on 16 August 2024.
Raw Data by Individual
Individual Datatype Bases Coverage Bytes Access
bGalGal1 PacBio CLR 123.49 Gbp 102.06x 213.3 GiB
PacBio HiFi (subreads) 1587.32 Gbp 1311.84x 2.7 TiB
PacBio HiFi (.fq) 92.89 Gbp 76.77x 79.4 GiB
PacBio HiFi (.bam) 261.07 Gbp 215.76x 0.9 TiB
Oxford Nanopore Simplex 191.42 Gbp 158.20x 160.4 GiB
10x 95.77 Gbp 79.15x 52.8 GiB
Bionano N/A 456.16x 1.0 GiB
Arima 106.22 Gbp 87.78x 63.1 GiB
bGalGal2 Arima 100.61 Gbp 83.15x 63.1 GiB
Illumina 103.18 Gbp 85.27x 51.7 GiB
bGalGal3 Arima 102.19 Gbp 84.45x 63.0 GiB
Illumina 116.18 Gbp 96.02x 58.0 GiB
bGalGal4 PacBio HiFi (subreads) 803.98 Gbp 664.44x 1.4 TiB
PacBio HiFi (.bam) 39.38 Gbp 32.55x 33.7 GiB
10x 78.41 Gbp 64.80x 39.1 GiB
Bionano N/A 319.58x 802.4 MiB
Arima 79.34 Gbp 65.57x 52.5 GiB
bGalGal5 PacBio HiFi (subreads) 733.80 Gbp 606.45x 1.3 TiB
PacBio HiFi (.fq, Q≥20) 0.00x 33.8 GiB
10x 104.31 Gbp 86.21x 51.6 GiB
Bionano N/A 459.32x 0.9 GiB
Arima 147.73 Gbp 122.09x 89.6 GiB
Bases and Coverage are approximate.
Coverage based on genome size 1.21 Gbp.
Last upload on 16 August 2024.
Assemblies
Individual 1 Maternal Assembly
Version assembly_rockefeller_trio_1.6 from 17 October 2019
bGalGal1.mat.asm.20191017.fasta.gz (285.8 MiB)

Quality: 54.4 errors/Mb (QV=42.64)

Contigs Scaffolds
NG LG Len LG Len
10 1 65.39 Mbp 0 147.88 Mbp
20 4 29.02 Mbp 1 110.93 Mbp
30 9 23.81 Mbp 3 90.31 Mbp
40 14 22.53 Mbp 4 74.16 Mbp
50 21 16.50 Mbp 6 34.59 Mbp
60 31 9.96 Mbp 11 20.07 Mbp
70 48 4.80 Mbp 18 13.97 Mbp
80 402 73.42 Kbp 33 5.23 Mbp
90 0 0
100 0 0
0.816x 863 0.99 Gbp 600 1.05 Gbp
NG based on genome size 1.21 Gbp.
Individual 1 Paternal Assembly
Version assembly_rockefeller_trio_1.6 from 17 October 2019
bGalGal1.pat.asm.20191017.fasta.gz (302.8 MiB)

Quality: 62.6 errors/Mb (QV=42.03)

Contigs Scaffolds
NG LG Len LG Len
10 2 48.49 Mbp 0 148.33 Mbp
20 5 34.45 Mbp 1 110.73 Mbp
30 9 23.49 Mbp 3 90.04 Mbp
40 15 19.68 Mbp 4 85.71 Mbp
50 22 14.98 Mbp 5 74.41 Mbp
60 31 10.49 Mbp 8 35.80 Mbp
70 45 6.21 Mbp 14 17.75 Mbp
80 83 1.29 Mbp 24 6.02 Mbp
90 0 0
100 0 0
0.861x 738 1.04 Gbp 485 1.06 Gbp
NG based on genome size 1.21 Gbp.
Individual 1 Mitochondrial Assembly
Version assembly_MT_rockefeller from 2 October 2019
bGalGal1.MT.20191002.fasta.gz (5.2 KiB)

Quality: not computed
Individual 4 Primary Assembly
Version assembly_curated from 4 October 2021
bGalGal4.pri.cur.20211004.fasta.gz (306.0 MiB)

Quality: 27.6 errors/Mb (QV=45.59)

Contigs Scaffolds
NG LG Len LG Len
10 5 18.83 Mbp 0 199.11 Mbp
20 12 13.80 Mbp 1 150.57 Mbp
30 23 9.97 Mbp 2 113.04 Mbp
40 38 6.62 Mbp 3 91.56 Mbp
50 59 4.53 Mbp 4 80.14 Mbp
60 92 3.01 Mbp 6 36.75 Mbp
70 145 1.85 Mbp 11 21.28 Mbp
80 238 0.95 Mbp 18 11.63 Mbp
90 721 34.93 Kbp 108 70.68 Kbp
100 0 0
0.902x 812 1.09 Gbp 246 1.09 Gbp
NG based on genome size 1.21 Gbp.
Individual 4 Alternate Assembly
Version assembly_curated from 4 October 2021
bGalGal4.alt.cur.20211004.fasta.gz (254.0 MiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 53 1.68 Mbp 53 1.68 Mbp
20 137 1.23 Mbp 137 1.23 Mbp
30 254 0.91 Mbp 254 0.91 Mbp
40 406 0.69 Mbp 406 0.69 Mbp
50 617 479.35 Kbp 617 479.35 Kbp
60 930 298.50 Kbp 930 298.50 Kbp
70 1681 68.54 Kbp 1681 68.54 Kbp
80 0 0
90 0 0
100 0 0
0.732x 2684 0.89 Gbp 2683 0.89 Gbp
NG based on genome size 1.21 Gbp.
Individual 4 Mitochondrial Assembly
Version assembly_MT_rockefeller from 13 December 2022
bGalGal4.MT.20221213.fasta.gz (5.0 KiB)

Quality: not computed
Individual 5 Primary Assembly
Version assembly_curated from 20 September 2021
bGalGal5.pri.cur.20210920.fasta.gz (309.3 MiB)

Quality: 0.5 errors/Mb (QV=62.68)

Contigs Scaffolds
NG LG Len LG Len
10 4 24.49 Mbp 0 199.38 Mbp
20 10 14.91 Mbp 1 151.02 Mbp
30 19 12.54 Mbp 2 111.84 Mbp
40 29 10.41 Mbp 3 91.65 Mbp
50 43 7.06 Mbp 4 87.48 Mbp
60 65 4.50 Mbp 6 37.65 Mbp
70 99 2.86 Mbp 10 21.81 Mbp
80 161 1.36 Mbp 17 12.85 Mbp
90 347 147.21 Kbp 41 0.98 Mbp
100 0 0
0.915x 712 1.11 Gbp 252 1.11 Gbp
NG based on genome size 1.21 Gbp.
Individual 5 Alternate Assembly
Version assembly_curated from 20 September 2021
bGalGal5.alt.cur.20210920.fasta.gz (260.2 MiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 36 2.43 Mbp 36 2.43 Mbp
20 97 1.73 Mbp 97 1.73 Mbp
30 178 1.30 Mbp 178 1.30 Mbp
40 290 0.93 Mbp 289 0.94 Mbp
50 447 0.63 Mbp 446 0.63 Mbp
60 681 419.62 Kbp 679 419.80 Kbp
70 1142 146.71 Kbp 1141 146.91 Kbp
80 0 0
90 0 0
100 0 0
0.754x 2263 0.91 Gbp 2259 0.91 Gbp
NG based on genome size 1.21 Gbp.
Individual 5 Mitochondrial Assembly
Version assembly_MT_rockefeller from 13 December 2022
bGalGal5.MT.20221213.fasta.gz (5.0 KiB)

Quality: not computed
Assembly Metadata
bGalGal4_metadata.yml (view)
data:
  pacbio:
    data:
    - mean_length (bp): 19543.0
      name: m54306U_200113_164216.Q20.fastq
      reads: 66738
      yield (bp): 1304276109
    - mean_length (bp): 18851.0
      name: m64055_200702_205110.Q20.fastq
      reads: 102154
      yield (bp): 1925750278
    - mean_length (bp): 14657.0
      name: m54306U_201011_031056.Q20.fastq
      reads: 137064
      yield (bp): 2009010721
    - mean_length (bp): 14715.0
      name: m64055_201028_023638.Q20.fastq
      reads: 92886
      yield (bp): 1366899272
    - mean_length (bp): 15195.0
      name: m64055_200925_152947.Q20.fastq
      reads: 288693
      yield (bp): 4386926953
    - mean_length (bp): 13533.0
      name: m54306U_201106_204219.Q20.fastq
      reads: 63591
      yield (bp): 860584721
    - mean_length (bp): 15895.0
      name: m64055_210307_103726.Q20.fastq
      reads: 731596
      yield (bp): 11629223407
    - mean_length (bp): 16508.0
      name: m64055_210315_104802.Q20.fastq
      reads: 509934
      yield (bp): 8417992604
    - mean_length (bp): 16393.0
      name: m54306U_210322_154536.Q20.fastq
      reads: 439173
      yield (bp): 7199604271
    metadata:
    - name: m54306U_200113_164216.Q20.fastq
      datatype: hifi
    - name: m64055_200702_205110.Q20.fastq
      datatype: hifi
    - name: m54306U_201011_031056.Q20.fastq
      datatype: hifi
    - name: m64055_201028_023638.Q20.fastq
      datatype: hifi
    - name: m64055_200925_152947.Q20.fastq
      datatype: hifi
    - name: m54306U_201106_204219.Q20.fastq
      datatype: hifi
    - name: m64055_210307_103726.Q20.fastq
      datatype: hifi
    - name: m64055_210315_104802.Q20.fastq
      datatype: hifi
    - name: m54306U_210322_154536.Q20.fastq
      datatype: hifi
    summary:
      yield (bp): 39100268336
      reads: 2431829
      coverage (X): 32.31
  bionano:
    data:
      molecules:
      - name: bGalGal4_Saphyr_DLE1_3680518.bnx.gz
        yield (bp): 200845200000.0
        N50 (kb): 266.2
        density (labels/100kb): 18.69
      cmaps:
      - name: bGalGal4_Saphyr_DLE1_3680542.cmap
        length (Mb): 1108.338
        N50 (Mb): 22.779
    metadata:
    - name: bGalGal4_Saphyr_DLE1_3680518.bnx.gz
      enzyme: DLE1
    summary:
      yield (bp): 200845200000
      coverage (X): 165.99
  hic:
  - no stats found
biosamples:
- common_name: chicken
  taxon_Id: '9031'
  bioproject_accession: ''
  organism: Gallus gallus
  isolate: bGalGal4
  breed: Ross
  dev_stage: juvenile
  sex: female
  tissue: ''
  biomaterial_provider: University of Copenhagen
  collection_date: '2019-10-17'
  collected_by: 'Joan Tarradas '
  birth_date: ''
  birth_location: ''
  lat_lon: ''
  store_cond: -80C
  treatment: Preserved EDTA + 1mL ethanol
  description: ''
  specimen_voucher: ''
  geo_loc_name: Spain
  tube_id: bGalGal4.BL1,bGalGal4.BL2,bGalGal4.BL3,bGalGal4.BL4
assembly:
- no sw yaml file found
vgp_assembly_2.0/bGalGal4.yaml (view)
species: Gallus gallus
specimen: bGalGal4
projects:
  - vgp
primary: s3://genomeark/species/Gallus_gallus/bGalGal4/vgp_assembly_2.0/bGalGal4.pri.asm.20210619.fasta.gz
pretext: s3://genomeark/species/Gallus_gallus/bGalGal4/vgp_assembly_2.0/evaluation/pretext/s2/bGalGal4_s2.pretext
haplotigs: s3://genomeark/species/Gallus_gallus/bGalGal4/vgp_assembly_2.0/bGalGal4.alt.asm.20210619.fasta.gz
kmer_spectra_img: s3://genomeark/species/Gallus_gallus/bGalGal4/vgp_assembly_2.0/evaluation/bGalGal4.PRIvsALT/04_merquryQVandKAT/bGalGal4.PRIvsALT_merqOutput.spectra-cn.st.png
pacbio_read_dir:  s3://genomeark/species/Gallus_gallus/bGalGal4/genomic_data/pacbio_hifi/
pacbio_read_type: hifi
hic_read_dir:  s3://genomeark/species/Gallus_gallus/bGalGal4/genomic_data/arima/
pipeline:
  - hifiasm (0.14)
  - purge_dups (1.2.5)
  - bionano solve (Solve3.6.1_11162020)
  - salsa (2.2)
assembled_by_group: BeGenDiv
notes: This assembly was run with the standard hifiasm pipeline (ie, pseudohaplotype) with no hifiasm internal purging set. Smrt-bell adapter sequences removed from HiFi reads with cutadapt. Purge_dups was used instead for purging and phasing. No polishing has been performed. There was also no mitochondrial genome used, so alternate assembly is equivalent of q2 in pipeline. Kmer spectra analysis performed using 10x reads.
bGalGal5_metadata.yml (view)
data:
  pacbio:
  - no stats foun
  bionano:
    data:
      molecules:
      - name: bGalGal5_Saphyr_DLE1_3680519.bnx.gz
        yield (bp): 209101300000.0
        N50 (kb): 235.5
        density (labels/100kb): 14.44
      cmaps:
      - name: bGalGal5_Saphyr_DLE1_3680543.cmap
        length (Mb): 1152.308
        N50 (Mb): 48.052
    metadata:
    - name: bGalGal5_Saphyr_DLE1_3680519.bnx.gz
      enzyme: DLE1
    summary:
      yield (bp): 209101300000
      coverage (X): 172.81
  hic:
  - no stats found
biosamples:
- common_name: chicken
  taxon_Id: '9031'
  bioproject_accession: ''
  organism: Gallus gallus
  isolate: bGalGal5
  breed: Cobb
  dev_stage: juvenile
  sex: female
  tissue: blood
  biomaterial_provider: University of Copenhagen
  collection_date: '2019-10-17'
  collected_by: 'Joan Tarradas '
  birth_date: ''
  birth_location: ''
  lat_lon: ''
  store_cond: -80C
  treatment: Preserved EDTA + 1mL ethanol
  description: ''
  specimen_voucher: ''
  geo_loc_name: Spain
  tube_id: bGalGal5.BL1
assembly:
- no sw yaml file found
vgp_assembly_2.0/bGalGal5.yaml (view)
species: Gallus gallus
specimen: bGalGal5
projects:
  - vgp
primary: s3://genomeark/species/Gallus_gallus/bGalGal5/vgp_assembly_2.0/bGalGal5.pri.asm.20210412.fasta.gz
pretext: s3://genomeark/species/Gallus_gallus/bGalGal5/vgp_assembly_2.0/evaluation/pretext/s2/bGalGal5_s2.pretext
haplotigs: s3://genomeark/species/Gallus_gallus/bGalGal5/vgp_assembly_2.0/bGalGal5.alt.asm.20210412.fasta.gz
kmer_spectra_img: s3://genomeark/species/Gallus_gallus/bGalGal5/vgp_assembly_2.0/evaluation/bGalGal5.PRIvsALT/04_merquryQVandKAT/bGalGal5.PRIvsALT_merqOutput.spectra-cn.st.png
pacbio_read_dir:  s3://genomeark/species/Gallus_gallus/bGalGal5/genomic_data/pacbio_hifi/
pacbio_read_type: hifi
hic_read_dir:  s3://genomeark/species/Gallus_gallus/bGalGal5/genomic_data/arima/
pipeline:
  - hifiasm (0.14)
  - purge_dups (1.2.5)
  - bionano solve (Solve3.6.1_11162020)
  - salsa (2.2)
assembled_by_group: BeGenDiv
notes: This assembly was run with the standard hifiasm pipeline (ie, pseudohaplotype) with no hifiasm internal purging set. Smrt-bell adapter sequences removed from HiFi reads with cutadapt. Purge_dups was used instead for purging and phasing. No polishing has been performed. There was also no mitochondrial genome used, so alternate assembly is equivalent of q2 in pipeline. Kmer spectra analysis performed using 10x reads.
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.