Haemorhous mexicanus

house finch

Included in the VGP.

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


Resource Primary Assembly Alternate Assembly
GenBank bHaeMex1: GCA_027477595.1 bHaeMex1: GCA_027406555.1
ENA bHaeMex1: GCA_027477595.1 bHaeMex1: GCA_027406555.1
UCSC Genome Browser bHaeMex1: GCA_027477595.1 bHaeMex1: GCA_027406555.1

metadata.yaml (view) (edit on github)
species:
  name: Haemorhous mexicanus
  individuals:
  - short_name: bHaeMex1
  short_name: bHaeMex
  taxon_id: '30427'
  common_name: house finch
  genome_size: 1369000000
  genome_size_method: GoAT
  order:
    name: Passeriformes
  family:
    name: Fringillidae
  project: [ vgp ]
CC BY 2.0 Nigel (flickr)
Raw Data by Technology
Datatype Individual Bases Coverage Bytes Access
PacBio HiFi (subreads) bHaeMex1 512.18 Gbp 374.13x 1.0 TiB
PacBio HiFi (.fq) bHaeMex1 50.45 Gbp 36.85x 37.4 GiB
Bionano bHaeMex1 N/A 430.47x 0.9 GiB
Arima bHaeMex1 218.60 Gbp 159.68x 99.6 GiB
Bases and Coverage are approximate.
Coverage based on genome size 1.37 Gbp.
Last upload on 3 May 2022.
Raw Data by Individual
Individual Datatype Bases Coverage Bytes Access
bHaeMex1 PacBio HiFi (subreads) 512.18 Gbp 374.13x 1.0 TiB
PacBio HiFi (.fq) 50.45 Gbp 36.85x 37.4 GiB
Bionano N/A 430.47x 0.9 GiB
Arima 218.60 Gbp 159.68x 99.6 GiB
Bases and Coverage are approximate.
Coverage based on genome size 1.37 Gbp.
Last upload on 3 May 2022.
Assemblies
Individual 1 Primary Assembly
Version assembly_curated from 3 February 2022
bHaeMex1.pri.cur.20220203.fasta.gz (320.1 MiB)

Quality: 0.5 errors/Mb (QV=63.16)

Contigs Scaffolds
NG LG Len LG Len
10 2 44.30 Mbp 0 159.31 Mbp
20 6 29.77 Mbp 1 122.82 Mbp
30 12 21.31 Mbp 3 89.32 Mbp
40 19 16.93 Mbp 4 78.19 Mbp
50 28 13.36 Mbp 6 66.87 Mbp
60 40 9.46 Mbp 10 26.78 Mbp
70 61 4.08 Mbp 16 17.44 Mbp
80 126 0.83 Mbp 27 7.00 Mbp
90 0 0
100 0 0
0.831x 478 1.14 Gbp 183 1.15 Gbp
NG based on genome size 1.37 Gbp.
Individual 1 Alternate Assembly
Version assembly_curated from 3 February 2022
bHaeMex1.alt.cur.20220203.fasta.gz (294.3 MiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 7 13.45 Mbp 7 13.45 Mbp
20 20 9.30 Mbp 20 9.30 Mbp
30 39 6.23 Mbp 39 6.23 Mbp
40 66 4.17 Mbp 66 4.17 Mbp
50 105 2.94 Mbp 105 2.94 Mbp
60 168 1.69 Mbp 168 1.69 Mbp
70 304 0.55 Mbp 304 0.55 Mbp
80 0 0
90 0 0
100 0 0
0.759x 1004 1.04 Gbp 1003 1.04 Gbp
NG based on genome size 1.37 Gbp.
Assembly Metadata
assembly_vgp_standard_2.0/bHaeMex1.yaml (view)
species: Haemorhous mexicanus
specimen: bHaeMex1
projects:
  - vgp
primary: s3://genomeark/species/Haemorhous_mexicanus/bHaeMex1/assembly_vgp_standard_2.0/bHaeMex1.pri.asm.20210901.fasta.gz
haplotigs: s3://genomeark/species/Haemorhous_mexicanus/bHaeMex1/assembly_vgp_standard_2.0/bHaeMex1.alt.asm.20210820.fasta.gz
hic_bam: s3://genomeark/species/Haemorhous_mexicanus/bHaeMex1/assembly_vgp_standard_2.0/evaluation/pretext/s2/bHaeMex1_s2.bam
pretext: s3://genomeark/species/Haemorhous_mexicanus/bHaeMex1/assembly_vgp_standard_2.0/evaluation/pretext/s2/bHaeMex1_s2.pretext
kmer_spectra_img: s3://genomeark/species/Haemorhous_mexicanus/bHaeMex1/assembly_vgp_standard_2.0/evaluation/merqury/p/bHaeMex1_images/output_merqury.spectra-cn.fl.png
pipeline:
  - hifiasm (0.15.4+galaxy)
  - purge_dups (1.2.5+galaxy3)
  - bionano_solve (3.6.1+galaxy2)
  - salsa (2.3+galaxy0)
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.