Ammodramus caudacutus

saltmarsh sparrow

Included in the VGP.

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


Resource Primary Assembly Alternate Assembly
GenBank bAmmCau1: GCA_027887145.1 bAmmCau1: GCA_027887135.1
ENA bAmmCau1: GCA_027887145.1 bAmmCau1: GCA_027887135.1
UCSC Genome Browser bAmmCau1: GCA_027887145.1 bAmmCau1: GCA_027887135.1

metadata.yaml (view) (edit on github)
species:
  name: Ammodramus caudacutus
  individuals:
  - short_name: bAmmCau1
  short_name: bAmmCau
  taxon_id: 69262
  common_name: saltmarsh sparrow
  genome_size: 1306000000
  genome_size_method: GoAT
  order:
    name: Passeriformes
  family:
    name: Passerellidae
  project: [ vgp ]
CC BY-SA 3.0 Wolfgang Wander (Wikimedia)
Raw Data by Technology
Datatype Individual Bases Coverage Bytes Access
PacBio HiFi (subreads) bAmmCau1 250.59 Gbp 191.87x 540.1 GiB
PacBio HiFi (.fq) bAmmCau1 44.64 Gbp 34.18x 32.6 GiB
PacBio HiFi (.bam) bAmmCau1 44.44 Gbp 34.03x 152.0 GiB
Bionano bAmmCau1 N/A 450.73x 0.9 GiB
Arima bAmmCau1 147.42 Gbp 112.88x 73.2 GiB
Bases and Coverage are approximate.
Coverage based on genome size 1.31 Gbp.
Last upload on 3 May 2022.
Raw Data by Individual
Individual Datatype Bases Coverage Bytes Access
bAmmCau1 PacBio HiFi (subreads) 250.59 Gbp 191.87x 540.1 GiB
PacBio HiFi (.fq) 44.64 Gbp 34.18x 32.6 GiB
PacBio HiFi (.bam) 44.44 Gbp 34.03x 152.0 GiB
Bionano N/A 450.73x 0.9 GiB
Arima 147.42 Gbp 112.88x 73.2 GiB
Bases and Coverage are approximate.
Coverage based on genome size 1.31 Gbp.
Last upload on 3 May 2022.
Assemblies
Individual 1 Primary Assembly
Version assembly_curated from 22 April 2022
bAmmCau1.pri.cur.20220422.fasta.gz (329.6 MiB)

Quality: 0.5 errors/Mb (QV=63.15)

Contigs Scaffolds
NG LG Len LG Len
10 3 24.21 Mbp 0 157.15 Mbp
20 10 17.54 Mbp 1 122.01 Mbp
30 18 14.61 Mbp 2 119.29 Mbp
40 28 10.57 Mbp 4 78.53 Mbp
50 42 7.54 Mbp 6 66.58 Mbp
60 63 5.28 Mbp 8 44.36 Mbp
70 93 3.54 Mbp 12 22.58 Mbp
80 142 1.91 Mbp 19 13.15 Mbp
90 265 486.75 Kbp 37 2.23 Mbp
100 0 0
0.948x 645 1.24 Gbp 282 1.24 Gbp
NG based on genome size 1.31 Gbp.
Individual 1 Alternate Assembly
Version assembly_curated from 22 April 2022
bAmmCau1.alt.cur.20220422.fasta.gz (319.7 MiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 43 2.21 Mbp 43 2.21 Mbp
20 115 1.55 Mbp 115 1.55 Mbp
30 214 1.15 Mbp 214 1.15 Mbp
40 340 0.91 Mbp 340 0.91 Mbp
50 504 0.70 Mbp 504 0.70 Mbp
60 725 0.51 Mbp 725 0.51 Mbp
70 1027 363.46 Kbp 1027 363.46 Kbp
80 1508 198.74 Kbp 1508 198.74 Kbp
90 0 0
100 0 0
0.893x 3054 1.17 Gbp 3054 1.17 Gbp
NG based on genome size 1.31 Gbp.
Assembly Metadata
assembly_vgp_standard_2.0/bAmmCau1.yaml (view)
species: Ammodramus caudacutus
specimen: bAmmCau1
projects:
 - vgp
primary: s3://genomeark/species/Ammodramus_caudacutus/bAmmCau1/assembly_vgp_standard_2.0/bAmmCau1.pri.asm.20220223.fasta.gz
haplotigs: s3://genomeark/species/Ammodramus_caudacutus/bAmmCau1/assembly_vgp_standard_2.0/bAmmCau1.alt.asm.20220223.fasta.gz
hic_bam: s3://genomeark/species/Ammodramus_caudacutus/bAmmCau1/assembly_vgp_standard_2.0/evaluation/pretext/s2/bAmmCau1_s2.bam
pretext: s3://genomeark/species/Ammodramus_caudacutus/bAmmCau1/assembly_vgp_standard_2.0/evaluation/pretext/s2/bAmmCau1_heatmap.pretext
kmer_spectra_img: s3://genomeark/species/Ammodramus_caudacutus/bAmmCau1/assembly_vgp_standard_2.0/evaluation/merqury/p/bAmmCau1_png/
pipeline:
  - hifiasm (0.15.4+galaxy0)
  - purge_dups (1.2.5+galaxy3)
  - solve (3.6.1+galaxy2)
  - 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.