Ammospiza nelsoni

Nelson's sparrow

Included in the VGP.

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


Resource Primary Assembly Alternate Assembly
GenBank bAmmNel1: GCA_027579445.1 bAmmNel1: GCA_027579665.1
ENA bAmmNel1: GCA_027579445.1 bAmmNel1: GCA_027579665.1
UCSC Genome Browser bAmmNel1: GCA_027579445.1 bAmmNel1: GCA_027579665.1

metadata.yaml (view) (edit on github)
species:
  name: Ammospiza nelsoni
  individuals:
  - short_name: bAmmNel1
  short_name: bAmmNel
  taxon_id: 2857394
  common_name: Nelson's sparrow
  genome_size: 1300000000
  genome_size_method: GoAT
  order:
    name: Passeriformes
  family:
    name: Passerellidae
  project: [ vgp ]
CC0 Chrissy McClarren and Andy Reago (Wikimedia)
Raw Data by Technology
Datatype Individual Bases Coverage Bytes Access
PacBio HiFi (subreads) bAmmNel1 262.77 Gbp 202.13x 563.4 GiB
PacBio HiFi (.fq) bAmmNel1 44.56 Gbp 34.27x 35.2 GiB
PacBio HiFi (.bam) bAmmNel1 44.37 Gbp 34.13x 153.3 GiB
Bionano bAmmNel1 N/A 320.03x 653.6 MiB
Arima bAmmNel1 143.86 Gbp 110.66x 71.7 GiB
Bases and Coverage are approximate.
Coverage based on genome size 1.30 Gbp.
Last upload on 3 May 2022.
Raw Data by Individual
Individual Datatype Bases Coverage Bytes Access
bAmmNel1 PacBio HiFi (subreads) 262.77 Gbp 202.13x 563.4 GiB
PacBio HiFi (.fq) 44.56 Gbp 34.27x 35.2 GiB
PacBio HiFi (.bam) 44.37 Gbp 34.13x 153.3 GiB
Bionano N/A 320.03x 653.6 MiB
Arima 143.86 Gbp 110.66x 71.7 GiB
Bases and Coverage are approximate.
Coverage based on genome size 1.30 Gbp.
Last upload on 3 May 2022.
Assemblies
Individual 1 Primary Assembly
Version assembly_curated from 29 April 2022
bAmmNel1.pri.cur.20220429.fasta.gz (324.5 MiB)

Quality: 0.5 errors/Mb (QV=63.04)

Contigs Scaffolds
NG LG Len LG Len
10 2 37.43 Mbp 0 155.45 Mbp
20 7 23.62 Mbp 1 120.72 Mbp
30 13 20.19 Mbp 2 115.51 Mbp
40 20 15.04 Mbp 4 76.63 Mbp
50 31 10.16 Mbp 6 65.40 Mbp
60 47 6.61 Mbp 9 36.57 Mbp
70 71 4.14 Mbp 14 21.55 Mbp
80 115 2.05 Mbp 21 12.24 Mbp
90 240 363.10 Kbp 49 1.04 Mbp
100 0 0
0.908x 292 1.18 Gbp 77 1.19 Gbp
NG based on genome size 1.30 Gbp.
Individual 1 Alternate Assembly
Version assembly_curated from 22 December 2022
bAmmNel1.alt.cur.20221222.fasta.gz (259.0 MiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 40 2.25 Mbp 40 2.25 Mbp
20 116 1.46 Mbp 116 1.46 Mbp
30 221 1.05 Mbp 221 1.05 Mbp
40 363 0.79 Mbp 363 0.79 Mbp
50 553 0.58 Mbp 553 0.58 Mbp
60 824 396.29 Kbp 824 396.29 Kbp
70 1261 213.51 Kbp 1261 213.51 Kbp
80 0 0
90 0 0
100 0 0
0.795x 2834 1.03 Gbp 2834 1.03 Gbp
NG based on genome size 1.30 Gbp.
Assembly Metadata
assembly_vgp_standard_2.0/bAmmNel1.yaml (view)
species: Ammospiza nelsoni
specimen: bAmmNel1
projects:
  - vgp
primary: s3://genomeark/species/Ammospiza_nelsoni/bAmmNel1/assembly_vgp_standard_2.0/bAmmNel1.pri.asm.20220222.fasta.gz
haplotigs: s3://genomeark/species/Ammospiza_nelsoni/bAmmNel1/assembly_vgp_standard_2.0/bAmmNel1.alt.asm.20220222.fasta.gz
hic_bam: s3://genomeark/species/Ammospiza_nelsoni/bAmmNel1/assembly_vgp_standard_2.0/evaluation/pretext/s2/bAmmNel1_s2.bam
pretext: s3://genomeark/species/Ammospiza_nelsoni/bAmmNel1/assembly_vgp_standard_2.0/evaluation/pretext/s2/bAmmNel1_heatmap.pretext
kmer_spectra_img: s3://genomeark/species/Ammospiza_nelsoni/bAmmNel1/assembly_vgp_standard_2.0/evaluation/merqury/p/bAmmNel1_png/
pipeline:
  - hifiasm (0.15.4+galaxy0)
  - purge_dups (1.2.5+galaxy3)
  - solve (3.6.1+galaxy3)
  - salsa (2.3+galaxy2)
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.