Ammospiza maritima

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Raw Data by Technology
Datatype Individual Bases Coverage Bytes Access
PacBio HiFi (subreads) bAmmMai1 968.31 Gbp 692.72x 1.7 TiB
PacBio HiFi (.fq) bAmmMai1 39.45 Gbp 28.22x 31.0 GiB
PacBio HiFi (.bam) bAmmMai1 111.25 Gbp 79.58x 389.8 GiB
Bionano bAmmMai1 N/A 369.88x 802.2 MiB
Arima bAmmMai1 141.58 Gbp 101.28x 71.1 GiB
Bases and Coverage are approximate.
Coverage based on genome size 1.40 Gbp.
Last upload on 27 September 2024.
Raw Data by Individual
Individual Datatype Bases Coverage Bytes Access
bAmmMai1 PacBio HiFi (subreads) 968.31 Gbp 692.72x 1.7 TiB
PacBio HiFi (.fq) 39.45 Gbp 28.22x 31.0 GiB
PacBio HiFi (.bam) 111.25 Gbp 79.58x 389.8 GiB
Bionano N/A 369.88x 802.2 MiB
Arima 141.58 Gbp 101.28x 71.1 GiB
Bases and Coverage are approximate.
Coverage based on genome size 1.40 Gbp.
Last upload on 27 September 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 12 18.44 Mbp 3 115.88 Mbp
30 20 15.70 Mbp 4 99.92 Mbp
40 30 12.94 Mbp 5 78.28 Mbp
50 43 8.74 Mbp 7 67.79 Mbp
60 63 6.03 Mbp 10 42.26 Mbp
70 91 3.86 Mbp 15 22.37 Mbp
80 137 2.31 Mbp 25 8.80 Mbp
90 224 1.15 Mbp 50 3.13 Mbp
100 865 12.48 Kbp 500 12.48 Kbp
1.000x 865 1.40 Gbp 500 1.40 Gbp
NG based on genome size 1.40 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 27 3.54 Mbp 27 3.54 Mbp
20 75 2.46 Mbp 75 2.46 Mbp
30 140 1.82 Mbp 140 1.82 Mbp
40 225 1.40 Mbp 225 1.40 Mbp
50 337 1.07 Mbp 337 1.07 Mbp
60 485 0.80 Mbp 485 0.80 Mbp
70 689 0.55 Mbp 689 0.55 Mbp
80 1005 335.79 Kbp 1005 335.79 Kbp
90 1628 137.35 Kbp 1627 137.38 Kbp
100 4332 126 bp 4329 7.46 Kbp
1.000x 4332 1.37 Gbp 4329 1.37 Gbp
NG based on genome size 1.40 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.