Ammodramus maritimus

seaside sparrow

Included in the VGP.

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


metadata.yaml (view) (edit on github)
species:
  name: Ammodramus maritimus
  individuals:
  - short_name: bAmmMai1
  short_name: bAmmMai
  taxon_id: 371905
  common_name: seaside sparrow
  genome_size: 1306000000
  genome_size_method: GoAT
  order:
    name: Passeriformes
  family:
    name: Passerellidae
  project: [ vgp ]
CC BY-SA 4.0 DMSDMS215 (Wikimedia)
Raw Data by Technology
Datatype Individual Bases Coverage Bytes Access
PacBio HiFi (subreads) bAmmMai1 968.31 Gbp 741.43x 1.7 TiB
PacBio HiFi (.fq) bAmmMai1 39.45 Gbp 30.20x 31.0 GiB
PacBio HiFi (.bam) bAmmMai1 111.25 Gbp 85.18x 389.8 GiB
Bionano bAmmMai1 N/A 395.89x 802.2 MiB
Arima bAmmMai1 141.58 Gbp 108.40x 71.1 GiB
Bases and Coverage are approximate.
Coverage based on genome size 1.31 Gbp.
Last upload on 1 August 2024.
Raw Data by Individual
Individual Datatype Bases Coverage Bytes Access
bAmmMai1 PacBio HiFi (subreads) 968.31 Gbp 741.43x 1.7 TiB
PacBio HiFi (.fq) 39.45 Gbp 30.20x 31.0 GiB
PacBio HiFi (.bam) 111.25 Gbp 85.18x 389.8 GiB
Bionano N/A 395.89x 802.2 MiB
Arima 141.58 Gbp 108.40x 71.1 GiB
Bases and Coverage are approximate.
Coverage based on genome size 1.31 Gbp.
Last upload on 1 August 2024.
Assemblies
Individual 1 Primary Assembly
Version assembly_curated from 9 December 2023
bAmmMai1.pri.cur.20231209.fasta.gz (370.6 MiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 5 25.06 Mbp 1 160.94 Mbp
20 11 19.26 Mbp 2 118.53 Mbp
30 18 16.39 Mbp 3 115.88 Mbp
40 27 14.31 Mbp 5 78.28 Mbp
50 38 10.06 Mbp 7 67.79 Mbp
60 54 6.67 Mbp 9 43.47 Mbp
70 77 4.68 Mbp 13 25.16 Mbp
80 110 3.06 Mbp 19 15.70 Mbp
90 167 1.73 Mbp 32 7.01 Mbp
100 276 0.78 Mbp 74 1.43 Mbp
1.069x 865 1.40 Gbp 500 1.40 Gbp
NG based on genome size 1.31 Gbp.
Individual 1 Alternate Assembly
Version assembly_curated from 9 December 2023
bAmmMai1.alt.cur.20231209.fasta.gz (370.0 MiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 26 3.60 Mbp 26 3.60 Mbp
20 70 2.54 Mbp 70 2.54 Mbp
30 130 1.86 Mbp 130 1.86 Mbp
40 208 1.50 Mbp 208 1.50 Mbp
50 309 1.14 Mbp 309 1.14 Mbp
60 440 0.87 Mbp 440 0.87 Mbp
70 615 0.64 Mbp 615 0.64 Mbp
80 871 409.21 Kbp 871 409.21 Kbp
90 1302 213.93 Kbp 1302 214.11 Kbp
100 2442 59.84 Kbp 2440 59.86 Kbp
1.048x 4332 1.37 Gbp 4329 1.37 Gbp
NG based on genome size 1.31 Gbp.
Individual 1 Mitochondrial Assembly
Version assembly_MT_rockefeller from 9 May 2023
bAmmMai1.MT.20230509.fasta.gz (5.4 KiB)

Quality: not computed
Assembly Metadata
assembly_vgp_standard_2.0/bAmmMai1.yml (view)
species: Ammodramus maritimus
specimen: bAmmMai1
projects: 
  - vgp
data_location: S3
release_to: S3
primary: s3://genomeark/species/Ammodramus_maritimus/bAmmMai1/assembly_vgp_standard_2.0/bAmmMai1.standard.pri.20230512.fasta.gz
haplotigs: s3://genomeark/species/Ammodramus_maritimus/bAmmMai1/assembly_vgp_standard_2.0/bAmmMai1.standard.alt.20230512.fasta.gz
pretext: s3://genomeark/species/Ammodramus_maritimus/bAmmMai1/assembly_vgp_standard_2.0/evaluation/pri/pretext/bAmmMai1_pri__s2.heatmap.pretext
kmer_spectra_img: s3://genomeark/species/Ammodramus_maritimus/bAmmMai1/assembly_vgp_standard_2.0/evaluation/merqury/bAmmMai1_png/
mito: s3://genomeark/species/Ammodramus_maritimus/bAmmMai1/assembly_MT_rockefeller/bAmmMai1.MT.20230509.fasta.gz
pacbio_read_dir: s3://genomeark/species/Ammodramus_maritimus/bAmmMai1/genomic_data/pacbio_hifi/
pacbio_read_type: hifi
hic_read_dir: s3://genomeark/species/Ammodramus_maritimus/bAmmMai1/genomic_data/arima/
bionano_cmap_dir: s3://genomeark/species/Ammodramus_maritimus/bAmmMai1/genomic_data/bionano/
pipeline:
  - hifiasm (0.18.8+galaxy1)
  - solve (3.7)
  - yahs (1.2a.2+galaxy1)
assembled_by_group: Rockefeller
notes: This was a primary/alternate assembly of bAmmMai1 (VGL ID is bAmmMar1). 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.