Melospiza georgiana

Swamp sparrow

Included in the VGP.

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


Resource Primary Assembly Alternate Assembly
GenBank bMelGeo1: GCA_028018845.1 bMelGeo1: GCA_028019105.1
ENA bMelGeo1: GCA_028018845.1 bMelGeo1: GCA_028019105.1
UCSC Genome Browser bMelGeo1: GCA_028018845.1 bMelGeo1: GCA_028019105.1

metadata.yaml (view) (edit on github)
species:
  name: Melospiza georgiana
  individuals:
  - short_name: bMelGeo1
  short_name: bMelGeo
  taxon_id: 44398
  common_name: Swamp sparrow
  genome_size: 1457000000
  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) bMelGeo1 333.85 Gbp 229.14x 678.6 GiB
PacBio HiFi (.fq) bMelGeo1 46.01 Gbp 31.58x 35.1 GiB
PacBio HiFi (.bam) bMelGeo1 45.73 Gbp 31.39x 157.2 GiB
Bionano bMelGeo1 N/A 254.06x 492.8 MiB
Arima bMelGeo1 150.88 Gbp 103.56x 73.3 GiB
Bases and Coverage are approximate.
Coverage based on genome size 1.46 Gbp.
Last upload on 3 May 2022.
Raw Data by Individual
Individual Datatype Bases Coverage Bytes Access
bMelGeo1 PacBio HiFi (subreads) 333.85 Gbp 229.14x 678.6 GiB
PacBio HiFi (.fq) 46.01 Gbp 31.58x 35.1 GiB
PacBio HiFi (.bam) 45.73 Gbp 31.39x 157.2 GiB
Bionano N/A 254.06x 492.8 MiB
Arima 150.88 Gbp 103.56x 73.3 GiB
Bases and Coverage are approximate.
Coverage based on genome size 1.46 Gbp.
Last upload on 3 May 2022.
Assemblies
Individual 1 Primary Assembly
Version assembly_curated from 20 May 2022
bMelGeo1.pri.cur.20220520.fasta.gz (322.9 MiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 5 19.19 Mbp 0 155.04 Mbp
20 13 16.84 Mbp 2 116.06 Mbp
30 23 13.36 Mbp 3 83.43 Mbp
40 36 10.37 Mbp 5 74.25 Mbp
50 54 6.45 Mbp 7 41.11 Mbp
60 84 3.85 Mbp 12 23.94 Mbp
70 131 2.35 Mbp 20 13.65 Mbp
80 0 0
90 0 0
100 0 0
0.797x 276 1.16 Gbp 40 1.16 Gbp
NG based on genome size 1.46 Gbp.
Individual 1 Alternate Assembly
Version assembly_curated from 20 May 2022
bMelGeo1.alt.cur.20220520.fasta.gz (299.2 MiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 8 12.25 Mbp 8 12.25 Mbp
20 22 8.59 Mbp 22 8.59 Mbp
30 43 5.44 Mbp 43 5.44 Mbp
40 76 3.65 Mbp 76 3.65 Mbp
50 123 2.48 Mbp 123 2.48 Mbp
60 196 1.53 Mbp 196 1.53 Mbp
70 369 410.90 Kbp 369 410.90 Kbp
80 0 0
90 0 0
100 0 0
0.738x 862 1.08 Gbp 862 1.08 Gbp
NG based on genome size 1.46 Gbp.
Assembly Metadata
assembly_vgp_standard_2.0/bMelGeo1.yaml (view)
species: Melospiza georgiana
specimen: bMelGeo1
projects:
  - vgp
primary: s3://genomeark/species/Melospiza_georgiana/bMelGeo1/assembly_vgp_standard_2.0/bMelGeo1.pri.asm.20220411.fasta.gz
haplotigs: s3://genomeark/species/Melospiza_georgiana/bMelGeo1/assembly_vgp_standard_2.0/bMelGeo1.alt.asm.220220411.fasta.gz
hic_bam: s3://genomeark/species/Melospiza_georgiana/bMelGeo1/assembly_vgp_standard_2.0/evaluation/pretext/s2/bMelGeo1_s2.bam
pretext: s3://genomeark/species/Melospiza_georgiana/bMelGeo1/assembly_vgp_standard_2.0/evaluation/pretext/s2/bMelGeo1_heatmap.pretext
kmer_spectra_img: s3://genomeark/species/Melospiza_georgiana/bMelGeo1/assembly_vgp_standard_2.0/evaluation/merqury/p/bMelGeo1_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.