Sayornis phoebe

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Resource Primary Assembly Alternate Assembly
GenBank bSayPho2: GCA_051295625.1 bSayPho2: GCA_051295565.1
ENA bSayPho2: GCA_051295625.1 bSayPho2: GCA_051295565.1
UCSC Genome Browser bSayPho2: GCA_051295625.1 bSayPho2: GCA_051295565.1

No image
Raw Data by Technology
Datatype Individual Bases Coverage Bytes Access
PacBio HiFi (.fq) bSayPho3 67.64 Gbp N/A 31.5 GiB
PacBio HiFi (.bam) bSayPho3 69.41 Gbp N/A 224.4 GiB
Arima bSayPho3 108.31 Gbp N/A 57.7 GiB
Bases and Coverage are approximate.
Coverage based on genome size .
Last upload on 18 April 2025.
Raw Data by Individual
Individual Datatype Bases Coverage Bytes Access
bSayPho3 PacBio HiFi (.fq) 67.64 Gbp N/A 31.5 GiB
PacBio HiFi (.bam) 69.41 Gbp N/A 224.4 GiB
Arima 108.31 Gbp N/A 57.7 GiB
Bases and Coverage are approximate.
Coverage based on genome size .
Last upload on 18 April 2025.
Assemblies
Individual 3 Haplotype 1 Assembly
Version assembly_curated from 11 February 2026
bSayPho3.hap1.cur.20260211.fasta.gz (331.0 MiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 2 64.55 Mbp 1 118.75 Mbp
20 5 35.40 Mbp 2 116.42 Mbp
30 9 29.41 Mbp 4 74.93 Mbp
40 13 23.51 Mbp 5 74.68 Mbp
50 19 18.46 Mbp 7 64.62 Mbp
60 26 14.90 Mbp 9 43.22 Mbp
70 36 10.96 Mbp 13 23.56 Mbp
80 48 8.48 Mbp 18 21.34 Mbp
90 69 3.43 Mbp 26 12.50 Mbp
100 470 5.04 Kbp 260 13.64 Kbp
1.000x 470 1.18 Gbp 260 1.18 Gbp
NG based on genome size .
Individual 3 Haplotype 2 Assembly
Version assembly_curated from 11 February 2026
bSayPho3.hap2.cur.20260211.fasta.gz (271.7 MiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 3 41.14 Mbp 1 119.02 Mbp
20 5 38.53 Mbp 2 116.42 Mbp
30 8 29.42 Mbp 3 99.43 Mbp
40 12 25.37 Mbp 5 74.56 Mbp
50 17 21.39 Mbp 6 64.56 Mbp
60 23 15.27 Mbp 8 41.70 Mbp
70 32 9.45 Mbp 11 25.74 Mbp
80 43 7.86 Mbp 15 21.39 Mbp
90 61 4.22 Mbp 21 12.87 Mbp
100 264 704 bp 128 17.91 Kbp
1.000x 264 1.03 Gbp 128 1.03 Gbp
NG based on genome size .
Individual 3 Mitochondrial Assembly
Version assembly_MT_rockefeller from 12 May 2025
bSayPho3.MT.20250512.fasta.gz (5.5 KiB)

Quality: not computed
Assembly Metadata
assembly_vgp_HiC_2.0/bSayPho3.yml (view)
species: Sayornis phoebe
specimem: bSayPho3
projects:
  - vgp
assembled_by_group: Rockefeller
data_location: S3
release_to: S3
combine_for_curation: true
hap1: s3://genomeark/species/Sayornis_phoebe/bSayPho3/assembly_vgp_HiC_2.0/bSayPho3.HiC.hap1.20250519.fasta.gz
hap2: s3://genomeark/species/Sayornis_phoebe/bSayPho3/assembly_vgp_HiC_2.0/bSayPho3.HiC.hap2.20250519.fasta.gz
pretext_hap1: s3://genomeark/species/Sayornis_phoebe/bSayPho3/assembly_vgp_HiC_2.0/evaluation/hap1/pretext/bSayPho3_hap1__s2_heatmap.pretext
pretext_hap2: s3://genomeark/species/Sayornis_phoebe/bSayPho3/assembly_vgp_HiC_2.0/evaluation/hap2/pretext/bSayPho3_hap2__s2_heatmap.pretext
kmer_spectra_img: s3://genomeark/species/Sayornis_phoebe/bSayPho3/assembly_vgp_HiC_2.0/evaluation/merqury/bSayPho3_png/
pacbio_read_dir: s3://genomeark/species/Sayornis_phoebe/bSayPho3/genomic_data/pacbio_hifi/
pacbio_read_type: hifi
hic_read_dir: s3://genomeark/species/Sayornis_phoebe/bSayPho3/genomic_data/arima/
pipeline:
  - hifiasm (0.24.0+galaxy0)
  - yahs (1.2a.2+galaxy2)
notes: This was a Hifiasm-HiC assembly of bSayPho3 resulting in two haplotype assemblies. HiC data were generated using the Arima library prep kit, and require trimming the first 5 bp off from the 5' end of both read files. The restriction enzymes used were the Arima v2 kit, so the cutting sites are GATC, GANTC, CTNAG, TTAA.
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.