Sturnus vulgaris

Common starling

Included in the VGP.

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


metadata.yaml (view) (edit on github)
species:
  name: Sturnus vulgaris
  individuals:
  - short_name: bStuVul1
  short_name: bStuVul
  taxon_id: 9172
  common_name: Common starling
  genome_size: 1281000000
  genome_size_method: GoAT
  order:
    name: Passeriformes
  family:
    name: Sturnidae
  project: [ vgp ]
CC0 1.0 Bernard Spragg (flickr)
Raw Data by Technology
Datatype Individual Bases Coverage Bytes Access
PacBio HiFi (.fq) bStuVul1 49.38 Gbp 38.55x 37.5 GiB
PacBio HiFi (.bam) bStuVul1 150.83 Gbp 117.75x 522.8 GiB
Arima bStuVul1 64.33 Gbp 50.22x 33.1 GiB
Bases and Coverage are approximate.
Coverage based on genome size 1.28 Gbp.
Last upload on 12 August 2025.
Raw Data by Individual
Individual Datatype Bases Coverage Bytes Access
bStuVul1 PacBio HiFi (.fq) 49.38 Gbp 38.55x 37.5 GiB
PacBio HiFi (.bam) 150.83 Gbp 117.75x 522.8 GiB
Arima 64.33 Gbp 50.22x 33.1 GiB
Bases and Coverage are approximate.
Coverage based on genome size 1.28 Gbp.
Last upload on 12 August 2025.
Assemblies
Individual 1 Haplotype 1 Assembly
Version assembly_curated from 28 July 2025
bStuVul1.hap1.cur.20250728.fasta.gz (354.3 MiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 3 48.06 Mbp 1 156.82 Mbp
20 6 34.66 Mbp 2 119.41 Mbp
30 10 22.61 Mbp 3 115.32 Mbp
40 16 19.15 Mbp 5 74.94 Mbp
50 24 15.40 Mbp 7 73.11 Mbp
60 34 10.33 Mbp 9 42.05 Mbp
70 49 7.28 Mbp 13 22.91 Mbp
80 72 3.79 Mbp 20 15.13 Mbp
90 128 1.35 Mbp 31 7.90 Mbp
100 450 148.88 Kbp 130 299.85 Kbp
1.043x 1298 1.34 Gbp 1011 1.36 Gbp
NG based on genome size 1.28 Gbp.
Individual 1 Haplotype 2 Assembly
Version assembly_curated from 28 July 2025
bStuVul1.hap2.cur.20250728.fasta.gz (269.9 MiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 3 43.59 Mbp 1 158.36 Mbp
20 6 30.73 Mbp 2 141.62 Mbp
30 11 24.81 Mbp 3 119.93 Mbp
40 17 21.28 Mbp 5 74.17 Mbp
50 24 11.98 Mbp 7 41.48 Mbp
60 37 7.79 Mbp 11 22.76 Mbp
70 60 3.59 Mbp 18 14.15 Mbp
80 173 332.87 Kbp 32 6.24 Mbp
90 0 0
100 0 0
0.833x 576 1.07 Gbp 367 1.10 Gbp
NG based on genome size 1.28 Gbp.
Assembly Metadata
assembly_vgp_HiC_2.0/bStuVul1.yml (view)
species: Sturnus vulgaris
specimen: bStuVul1
projects: 
  - vgp
assembled_by_group: Rockefeller
data_location: S3
release_to: S3
combine_for_curation: true
hap1: s3://genomeark/species/Sturnus_vulgaris/bStuVul1/assembly_vgp_HiC_2.0/bStuVul1.HiC.hap1.20240422.fasta.gz
hap2: s3://genomeark/species/Sturnus_vulgaris/bStuVul1/assembly_vgp_HiC_2.0/bStuVul1.HiC.hap2.20240422.fasta.gz
pretext_hap1: s3://genomeark/species/Sturnus_vulgaris/bStuVul1/assembly_vgp_HiC_2.0/evaluation/hap1/pretext/bStuVul1_hap1_s2.pretext
pretext_hap2: s3://genomeark/species/Sturnus_vulgaris/bStuVul1/assembly_vgp_HiC_2.0/evaluation/hap2/pretext/bStuVul1_hap2_s2.pretext
kmer_spectra_img: s3://genomeark/species/Sturnus_vulgaris/bStuVul1/assembly_vgp_HiC_2.0/evaluation/merqury/bStuVul1_png/
pacbio_read_dir: s3://genomeark/species/Sturnus_vulgaris/bStuVul1/genomic_data/pacbio_hifi/
pacbio_read_type: hifi
hic_read_dir: s3://genomeark/species/Sturnus_vulgaris/bStuVul1/genomic_data/arima/
bionano_cmap_dir: s3://genomeark/species/Sturnus_vulgaris/bStuVul1/genomic_data/bionano/
pipeline: 
  - hifiasm (0.19.8+galaxy0)
  - solve (3.7)
  - yahs (1.2a.2+galaxy1)
notes: This was a Hifiasm-HiC assembly of bStuVul1, resulting in two complete haplotypes. This sample did have Bionano. HiC scaffolding was performed with YaHS.  The HiC prep kit used was Swift-IDT library prep. 
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.