Taeniopygia guttata

zebra finch

Included in the VGP.

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


Resource Primary Assembly Alternate Assembly
GenBank bTaeGut1: GCA_003957565.4 bTaeGut2: GCA_009859065.2 bTaeGut1: GCA_003957525.2 bTaeGut2: GCA_009859025.1
ENA bTaeGut1: GCA_003957565.4 bTaeGut2: GCA_009859065.2 bTaeGut1: GCA_003957525.2 bTaeGut2: GCA_009859025.1
UCSC Genome Browser bTaeGut1: GCA_003957565.4 bTaeGut2: GCA_009859065.2 bTaeGut1: GCA_003957525.2 bTaeGut2: GCA_009859025.1

Resource Maternal Assembly Paternal Assembly
GenBank bTaeGut2: GCA_008822115.3 bTaeGut2: GCA_008822125.1
ENA bTaeGut2: GCA_008822115.3 bTaeGut2: GCA_008822125.1
UCSC Genome Browser bTaeGut2: GCA_008822115.3 bTaeGut2: GCA_008822125.1

metadata.yaml (view) (edit on github)
species:
  short_name: bTaeGut
  name: Taeniopygia guttata
  taxon_id: 59729
  common_name: zebra finch
  order:
    name: Passeriformes
  family:
    name: Estrildidae
  individuals:
    - short_name: bTaeGut1
    - short_name: bTaeGut2
    - short_name: bTaeGut3
    - short_name: bTaeGut4
    - short_name: bTaeGut5
  genome_size: 1035611271
  genome_size_method:
  project: [ vgp ]
CC BY 2.0 Keith Gerstung (wikimedia)
Raw Data by Technology
Datatype Individual Bases Coverage Bytes Access
PacBio CLR bTaeGut1 109.72 Gbp 105.95x 392.7 GiB
bTaeGut2 102.06 Gbp 98.55x 181.8 GiB
bTaeGut6 139.76 Gbp 134.96x 247.6 GiB
PacBio HiFi (subreads) bTaeGut2 485.43 Gbp 468.74x 0.9 TiB
PacBio HiFi (.fq) bTaeGut2 39.52 Gbp 38.16x 30.5 GiB
bTaeGut7 135.08 Gbp 130.43x 102.6 GiB
PacBio HiFi (.bam) bTaeGut2 47.60 Gbp 45.96x 76.0 GiB
10x bTaeGut1 98.70 Gbp 95.31x 59.5 GiB
bTaeGut2 107.06 Gbp 103.38x 64.3 GiB
bTaeGut3 116.87 Gbp 112.85x 58.5 GiB
bTaeGut4 127.78 Gbp 123.39x 64.1 GiB
Bionano bTaeGut1 N/A 287.16x 246.7 MiB
bTaeGut2 N/A 1994.36x 3.1 GiB
Arima bTaeGut1 152.55 Gbp 147.30x 79.0 GiB
bTaeGut2 99.04 Gbp 95.64x 47.6 GiB
bTaeGut7 62.73 Gbp 60.57x 29.8 GiB
Illumina bTaeGut3 66.06 Gbp 63.78x 35.2 GiB
bTaeGut4 68.24 Gbp 65.89x 36.5 GiB
bTaeGut7 114.02 Gbp 110.10x 52.2 GiB
bTaeGut8 50.87 Gbp 49.12x 24.2 GiB
bTaeGut9 76.25 Gbp 73.63x 36.6 GiB
Bases and Coverage are approximate.
Coverage based on genome size 1.04 Gbp.
Last upload on 28 March 2023.
Raw Data by Individual
Individual Datatype Bases Coverage Bytes Access
bTaeGut1 PacBio CLR 109.72 Gbp 105.95x 392.7 GiB
10x 98.70 Gbp 95.31x 59.5 GiB
Bionano N/A 287.16x 246.7 MiB
Arima 152.55 Gbp 147.30x 79.0 GiB
bTaeGut2 PacBio CLR 102.06 Gbp 98.55x 181.8 GiB
PacBio HiFi (subreads) 485.43 Gbp 468.74x 0.9 TiB
PacBio HiFi (.fq) 39.52 Gbp 38.16x 30.5 GiB
PacBio HiFi (.bam) 47.60 Gbp 45.96x 76.0 GiB
10x 107.06 Gbp 103.38x 64.3 GiB
Bionano N/A 1994.36x 3.1 GiB
Arima 99.04 Gbp 95.64x 47.6 GiB
bTaeGut3 10x 116.87 Gbp 112.85x 58.5 GiB
Illumina 66.06 Gbp 63.78x 35.2 GiB
bTaeGut4 10x 127.78 Gbp 123.39x 64.1 GiB
Illumina 68.24 Gbp 65.89x 36.5 GiB
bTaeGut6 PacBio CLR 139.76 Gbp 134.96x 247.6 GiB
bTaeGut7 PacBio HiFi (.fq) 135.08 Gbp 130.43x 102.6 GiB
Arima 62.73 Gbp 60.57x 29.8 GiB
Illumina 114.02 Gbp 110.10x 52.2 GiB
bTaeGut8 Illumina 50.87 Gbp 49.12x 24.2 GiB
bTaeGut9 Illumina 76.25 Gbp 73.63x 36.6 GiB
Bases and Coverage are approximate.
Coverage based on genome size 1.04 Gbp.
Last upload on 28 March 2023.
Assemblies
Individual 1 Primary Assembly
Version assembly_curated from 9 April 2021
bTaeGut1.pri.cur.20210409.fasta.gz (298.4 MiB)

Quality: 403.0 errors/Mb (QV=33.95)

Contigs Scaffolds
NG LG Len LG Len
10 2 31.08 Mbp 0 151.65 Mbp
20 6 19.96 Mbp 1 114.02 Mbp
30 12 14.78 Mbp 2 112.60 Mbp
40 20 10.77 Mbp 3 75.40 Mbp
50 30 9.02 Mbp 4 71.57 Mbp
60 43 7.18 Mbp 6 61.66 Mbp
70 59 5.53 Mbp 8 35.59 Mbp
80 84 3.41 Mbp 12 20.54 Mbp
90 128 1.67 Mbp 18 13.77 Mbp
100 0 0
0.997x 526 1.03 Gbp 197 1.04 Gbp
NG based on genome size 1.04 Gbp.
Individual 1 Alternate Assembly
Version assembly_curated from 9 April 2021
bTaeGut1.alt.cur.20210409.fasta.gz (256.6 MiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 5 13.57 Mbp 5 13.57 Mbp
20 16 7.62 Mbp 16 7.62 Mbp
30 32 5.49 Mbp 32 5.49 Mbp
40 55 3.92 Mbp 55 3.92 Mbp
50 87 2.52 Mbp 87 2.52 Mbp
60 141 1.51 Mbp 141 1.51 Mbp
70 230 0.84 Mbp 230 0.84 Mbp
80 494 156.43 Kbp 492 162.30 Kbp
90 0 0
100 0 0
0.857x 1656 0.89 Gbp 1646 0.89 Gbp
NG based on genome size 1.04 Gbp.
Individual 1 Mitochondrial Assembly
Version assembly_MT_rockefeller from 3 October 2019
bTaeGut1.MT.20191003.fasta.gz (5.0 KiB)

Quality: not computed
Individual 2 Primary Assembly
Version assembly_curated from 25 April 2022
bTaeGut2.pri.cur.20220425.fasta.gz (309.4 MiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 4 20.62 Mbp 0 146.55 Mbp
20 10 16.23 Mbp 1 115.72 Mbp
30 17 13.76 Mbp 2 114.80 Mbp
40 26 9.98 Mbp 3 90.41 Mbp
50 38 7.85 Mbp 4 72.88 Mbp
60 54 5.18 Mbp 6 61.98 Mbp
70 78 3.89 Mbp 8 37.17 Mbp
80 111 2.57 Mbp 11 21.60 Mbp
90 160 1.66 Mbp 17 15.47 Mbp
100 267 475.07 Kbp 27 6.67 Mbp
1.051x 730 1.09 Gbp 192 1.10 Gbp
NG based on genome size 1.04 Gbp.
Individual 2 Alternate Assembly
Version assembly_curated from 27 May 2022
bTaeGut2.alt.cur.20220527.fasta.gz (91.5 KiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 0 0
20 0 0
30 0 0
40 0 0
50 0 0
60 0 0
70 0 0
80 0 0
90 0 0
100 0 0
0.000x 1 306.07 Kbp 1 306.07 Kbp
NG based on genome size 1.04 Gbp.
Individual 2 Merged Trio Assembly
Version assembly_curated from 5 September 2022
bTaeGut2.hap1.W.cur.20220905.fasta.gz (327.9 MiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 5 17.84 Mbp 0 152.62 Mbp
20 11 14.12 Mbp 1 115.84 Mbp
30 19 11.96 Mbp 2 115.09 Mbp
40 29 9.69 Mbp 3 88.56 Mbp
50 40 8.22 Mbp 4 72.81 Mbp
60 55 5.82 Mbp 6 61.99 Mbp
70 76 4.23 Mbp 8 37.49 Mbp
80 105 3.05 Mbp 11 26.18 Mbp
90 146 1.97 Mbp 16 18.52 Mbp
100 216 1.05 Mbp 24 7.91 Mbp
1.122x 1091 1.16 Gbp 572 1.17 Gbp
NG based on genome size 1.04 Gbp.
Individual 2 Maternal Assembly
Version assembly_curated from 27 May 2022
bTaeGut2.mat.cur.20220527.fasta.gz (289.3 MiB)

Quality: 50.4 errors/Mb (QV=42.98)

Contigs Scaffolds
NG LG Len LG Len
10 4 19.63 Mbp 0 152.74 Mbp
20 10 14.47 Mbp 1 115.89 Mbp
30 18 11.64 Mbp 2 114.67 Mbp
40 28 9.52 Mbp 3 73.99 Mbp
50 39 8.47 Mbp 4 72.15 Mbp
60 53 6.75 Mbp 6 39.35 Mbp
70 73 4.10 Mbp 9 26.15 Mbp
80 103 2.77 Mbp 14 19.63 Mbp
90 158 1.30 Mbp 21 11.25 Mbp
100 0 0
0.984x 554 1.02 Gbp 206 1.02 Gbp
NG based on genome size 1.04 Gbp.
Individual 2 Paternal Assembly
Version assembly_curated from 24 January 2020
bTaeGut2.pat.cur.20200124.fasta.gz (298.1 MiB)

Quality: 46.6 errors/Mb (QV=43.32)

Contigs Scaffolds
NG LG Len LG Len
10 4 17.44 Mbp 0 151.90 Mbp
20 12 9.99 Mbp 1 114.38 Mbp
30 24 7.33 Mbp 2 111.45 Mbp
40 40 5.73 Mbp 3 78.98 Mbp
50 61 4.43 Mbp 4 71.34 Mbp
60 87 3.38 Mbp 6 61.90 Mbp
70 127 2.11 Mbp 8 34.84 Mbp
80 186 1.35 Mbp 12 20.43 Mbp
90 294 0.64 Mbp 18 13.71 Mbp
100 0 42 0.75 Mbp
0.992x 1036 1.03 Gbp 202 1.05 Gbp
NG based on genome size 1.04 Gbp.
Individual 2 Haplotype 1 Assembly
Version assembly_curated from 5 September 2022
bTaeGut2.hap1.cur.20220905.fasta.gz (319.8 MiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 5 17.84 Mbp 0 152.62 Mbp
20 11 14.12 Mbp 1 115.84 Mbp
30 19 11.96 Mbp 2 115.09 Mbp
40 29 9.69 Mbp 3 88.56 Mbp
50 40 8.22 Mbp 4 72.81 Mbp
60 56 5.44 Mbp 6 61.99 Mbp
70 78 4.07 Mbp 8 37.49 Mbp
80 108 2.90 Mbp 11 21.60 Mbp
90 153 1.75 Mbp 17 15.57 Mbp
100 236 0.82 Mbp 27 6.36 Mbp
1.089x 1060 1.13 Gbp 560 1.13 Gbp
NG based on genome size 1.04 Gbp.
Individual 2 Haplotype 2 Assembly
Version assembly_curated from 5 September 2022
bTaeGut2.hap2.cur.20220905.fasta.gz (293.7 MiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 4 21.11 Mbp 0 152.47 Mbp
20 9 16.12 Mbp 1 115.75 Mbp
30 17 12.54 Mbp 2 114.02 Mbp
40 26 9.52 Mbp 3 73.67 Mbp
50 38 8.00 Mbp 4 72.22 Mbp
60 52 6.50 Mbp 6 39.35 Mbp
70 73 3.95 Mbp 9 26.88 Mbp
80 105 2.57 Mbp 14 19.63 Mbp
90 157 1.46 Mbp 21 11.12 Mbp
100 487 33.46 Kbp 111 71.45 Kbp
1.002x 578 1.04 Gbp 255 1.04 Gbp
NG based on genome size 1.04 Gbp.
Individual 2 Mitochondrial Assembly
Version assembly_MT_rockefeller from 3 October 2019
bTaeGut2.MT.20191003.fasta.gz (5.0 KiB)

Quality: not computed
Assembly Metadata
assembly_vgp_hic_2.0/bTaeGut2_hic.yaml (view)
species: Taeniopygia guttata
specimen: bTaeGut2
projects:
  - vgp
hap1: s3://genomeark/species/Taeniopygia_guttata/bTaeGut2/assembly_vgp_hic_2.0/bTaeGut2.hic.hap1.s2.fasta
hap2: s3://genomeark/species/Taeniopygia_guttata/bTaeGut2/assembly_vgp_hic_2.0/bTaeGut2.hic.hap2.s2.fasta
hap1_hic_bam: s3://genomeark/species/Taeniopygia_guttata/bTaeGut2/assembly_vgp_hic_2.0/evaluation/pretext/s2/bTaeGut2.hic.hap1.s2.bam
hap2_hic_bam: s3://genomeark/species/Taeniopygia_guttata/bTaeGut2/assembly_vgp_hic_2.0/evaluation/pretext/s2/bTaeGut2.hic.hap2.s2.bam
hap1_pretext: s3://genomeark/species/Taeniopygia_guttata/bTaeGut2/assembly_vgp_hic_2.0/evaluation/pretext/s2/bTaeGut2.hic.hap1.s2.pretext
hap2_pretext: s3://genomeark/species/Taeniopygia_guttata/bTaeGut2/assembly_vgp_hic_2.0/evaluation/pretext/s2/bTaeGut2.hic.hap2.s2.pretext
kmer_spectra_img: s3://genomeark/species/Taeniopygia_guttata/bTaeGut2/assembly_vgp_hic_2.0/evaluation/merqury/contigs_10xKmersForChild/
pipeline:
  - hifiasm (0.16.1-r375)
  - purge_dups (1.2.5)
  - solve (3.6.1)
  - salsa (2.2, updated to commit ed76685)
assembly_vgp_standard_2.0/bTaeGut2.yaml (view)
species: Taeniopygia_guttata
specimen: bTaeGut2
projects:
  - vgp
primary: s3://genomeark/species/Taeniopygia_guttata/bTaeGut2/assembly_vgp_standard_2.0/bTaeGut2.pri.asm.20211014.fasta.gz
haplotigs: s3://genomeark/species/Taeniopygia_guttata/bTaeGut2/assembly_vgp_standard_2.0/bTaeGut2.alt.asm.20210927.fasta.gz
hic_bam: s3://genomeark/species/Taeniopygia_guttata/bTaeGut2/assembly_vgp_standard_2.0/evaluation/pretext/s2/bTaeGut2.bam
pretext: s3://genomeark/species/Taeniopygia_guttata/bTaeGut2/assembly_vgp_standard_2.0/evaluation/pretext/s2/bTaeGut2.pretext
kmer_spectra_img: s3://genomeark/species/Taeniopygia_guttata/bTaeGut2/assembly_vgp_standard_2.0/evaluation/merqury/p/output_merqury_p.spectra-cn.fl
pipeline:
  - hifiasm (0.15.4+galaxy)
  - purge_dups (1.2.5+galaxy3)
  - bionano_solve (3.6.1+galaxy2)
  - salsa (2.3+galaxy0)
assembly_vgp_trio_2.0/bTaeGut2_trio.yaml (view)
species: Taeniopygia guttata
specimen: bTaeGut2
projects:
  - vgp
mat: s3://genomeark/species/Taeniopygia_guttata/bTaeGut2/assembly_vgp_trio_2.0/bTaeGut2_trio.rebinned.hap2.s2.fasta.gz
pat: s3://genomeark/species/Taeniopygia_guttata/bTaeGut2/assembly_vgp_trio_2.0/bTaeGut2_trio.rebinned.hap1.s2.fasta.gz
mat_hic_bam: s3://genomeark/species/Taeniopygia_guttata/bTaeGut2/assembly_vgp_trio_2.0/intermediates/salsa/s2/bTaeGut2_trio.rebinned.hap2.s2.bam
pat_hic_bam: s3://genomeark/species/Taeniopygia_guttata/bTaeGut2/assembly_vgp_trio_2.0/intermediates/salsa/s2/bTaeGut2_trio.rebinned.hap1.s2.bam
mat_pretext: s3://genomeark/species/Taeniopygia_guttata/bTaeGut2/assembly_vgp_trio_2.0/intermediates/salsa/s2/bTaeGut2_trio.rebinned.hap2.s2.pretext
pat_pretext: s3://genomeark/species/Taeniopygia_guttata/bTaeGut2/assembly_vgp_trio_2.0/intermediates/salsa/s2/bTaeGut2_trio.rebinned.hap1.s2.pretext
kmer_spectra_img: s3://genomeark/species/Taeniopygia_guttata/bTaeGut2/assembly_vgp_trio_2.0/evaluation/merqury/purge_dups/
pipeline:
  - hifiasm (0.16.1-r375)
  - purge_dups (1.2.5)
  - solve (3.6.1)
  - salsa (2.2)
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.