Passerculus sandwichensis

Savannah sparrow

Included in the VGP.

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


Resource Primary Assembly Alternate Assembly
GenBank bPasSan1: GCA_022577445.1 bPasSan1: GCA_022578375.1
ENA bPasSan1: GCA_022577445.1 bPasSan1: GCA_022578375.1
UCSC Genome Browser bPasSan1: GCA_022577445.1 bPasSan1: GCA_022578375.1

metadata.yaml (view) (edit on github)
species:
  name: Passerculus sandwichensis
  individuals:
  - short_name: bPasSan1
  short_name: bPasSan
  taxon_id: '161624'
  common_name: Savannah sparrow
  genome_size: 1178000000
  genome_size_method: GoAT
  order:
    name: Passeriformes
  family:
    name: Passerellidae
  project: [ vgp ]
CC BY-SA 3.0 Simon Pierre Barrette (Wikimedia)
Raw Data by Technology
Datatype Individual Bases Coverage Bytes Access
PacBio HiFi (subreads) bPasSan2 843.93 Gbp 716.41x 1.5 TiB
PacBio HiFi (.fq) bPasSan2 54.58 Gbp 46.33x 41.6 GiB
Bionano bPasSan2 N/A 379.53x 724.5 MiB
Arima bPasSan2 147.82 Gbp 125.48x 71.9 GiB
Bases and Coverage are approximate.
Coverage based on genome size 1.18 Gbp.
Last upload on 7 March 2024.
Raw Data by Individual
Individual Datatype Bases Coverage Bytes Access
bPasSan2 PacBio HiFi (subreads) 843.93 Gbp 716.41x 1.5 TiB
PacBio HiFi (.fq) 54.58 Gbp 46.33x 41.6 GiB
Bionano N/A 379.53x 724.5 MiB
Arima 147.82 Gbp 125.48x 71.9 GiB
Bases and Coverage are approximate.
Coverage based on genome size 1.18 Gbp.
Last upload on 7 March 2024.
Assemblies
Individual 2 Primary Assembly
Version assembly_curated from 27 May 2023
bPasSan2.pri.cur.20230527.fasta.gz (350.7 MiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 3 40.42 Mbp 1 157.12 Mbp
20 6 36.31 Mbp 2 118.51 Mbp
30 9 30.40 Mbp 3 116.75 Mbp
40 13 25.23 Mbp 4 81.24 Mbp
50 18 21.43 Mbp 6 73.84 Mbp
60 24 16.94 Mbp 8 42.00 Mbp
70 33 11.27 Mbp 11 31.47 Mbp
80 45 8.23 Mbp 16 20.64 Mbp
90 62 5.72 Mbp 24 12.73 Mbp
100 88 2.73 Mbp 35 8.75 Mbp
1.076x 358 1.27 Gbp 109 1.27 Gbp
NG based on genome size 1.18 Gbp.
Individual 2 Alternate Assembly
Version assembly_curated from 27 May 2023
bPasSan2.alt.cur.20230527.fasta.gz (315.2 MiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 8 12.26 Mbp 8 12.26 Mbp
20 19 8.45 Mbp 19 8.45 Mbp
30 34 6.76 Mbp 34 6.87 Mbp
40 56 4.77 Mbp 55 4.84 Mbp
50 84 3.68 Mbp 83 3.70 Mbp
60 119 2.72 Mbp 119 2.72 Mbp
70 174 1.78 Mbp 173 1.79 Mbp
80 256 1.09 Mbp 254 1.14 Mbp
90 429 364.87 Kbp 412 445.14 Kbp
100 0 0
0.962x 1349 1.13 Gbp 1242 1.13 Gbp
NG based on genome size 1.18 Gbp.
Individual 2 Mitochondrial Assembly
Version assembly_MT_rockefeller from 7 March 2023
bPasSan2.MT.20230307.fasta.gz (5.4 KiB)

Quality: not computed
Assembly Metadata
assembly_vgp_standard_2.0/bPasSan2.yml (view)
species: Passerculus sandwichensis
specimen: bPasSan2
projects: 
  - vgp
data_location: S3
release_to: S3
primary: s3://genomeark/species/Passerculus_sandwichensis/bPasSan2/assembly_vgp_standard_2.0/bPasSan2.standard.pri.20230308.fasta.gz
haplotigs: s3://genomeark/species/Passerculus_sandwichensis/bPasSan2/assembly_vgp_standard_2.0/bPasSan2.standard.alt.20230308.fasta.gz
pretext: s3://genomeark/species/Passerculus_sandwichensis/bPasSan2/assembly_vgp_standard_2.0/evaluation/pri/pretext/bPasSan2_pri__s2.heatmap.pretext
kmer_spectra_img: s3://genomeark/species/Passerculus_sandwichensis/bPasSan2/assembly_vgp_standard_2.0/evaluation/merqury/bPasSan2_png/
mito: s3://genomeark/species/Passerculus_sandwichensis/bPasSan2/assembly_MT_rockefeller/bPasSan2.MT.20230307.fasta.gz
pacbio_read_dir: s3://genomeark/species/Passerculus_sandwichensis/bPasSan2/genomic_data/pacbio_hifi/
pacbio_read_type: hifi
hic_read_dir: s3://genomeark/species/Passerculus_sandwichensis/bPasSan2/genomic_data/arima/
bionano_cmap_dir: s3://genomeark/species/Passerculus_sandwichensis/bPasSan2/genomic_data/bionano/
pipeline:
  - hifiasm (0.18.8+galaxy1)
  - solve (3.7)
  - yahs (1.2a.2+galaxy0)
assembled_by_group: Rockefeller
notes: This was a primary/alternate assembly of bPasSan2 (VGL-bPasSan1). This individual had bionano data. HiC scaffolding was performed with yahs. The HiC prep was Arima kit 2. This sample arrived with metadata indicating it is a female. 
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.