Trogon surrucura

Suruca trogon

Included in the VGP.

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


Resource Primary Assembly Alternate Assembly
GenBank bTroSur1: GCA_020746105.1 bTroSur1: GCA_020746095.1
ENA bTroSur1: GCA_020746105.1 bTroSur1: GCA_020746095.1
UCSC Genome Browser bTroSur1: GCA_020746105.1 bTroSur1: GCA_020746095.1

metadata.yaml (view) (edit on github)
species:
  short_name: bTroSur
  name: Trogon surrucura
  taxon_id: 297711
  common_name: Suruca trogon
  order:
    name: Trogoniformes
  family:
    name: Trogonidae
  individuals:
    - short_name: bTroSur1
  genome_size: 1000000000
  genome_size_method:
  project: [ vgp ]
CC BY 2.0 Afonso de Bragança (flickr)
Raw Data by Technology
Datatype Individual Bases Coverage Bytes Access
PacBio CLR bTroSur1 108.40 Gbp 108.40x 193.8 GiB
10x bTroSur1 151.40 Gbp 151.40x 74.5 GiB
Bionano bTroSur1 N/A 646.50x 1.4 GiB
Arima bTroSur1 98.51 Gbp 98.51x 67.9 GiB
Bases and Coverage are approximate.
Coverage based on genome size 1.00 Gbp.
Last upload on 19 April 2021.
Raw Data by Individual
Individual Datatype Bases Coverage Bytes Access
bTroSur1 PacBio CLR 108.40 Gbp 108.40x 193.8 GiB
10x 151.40 Gbp 151.40x 74.5 GiB
Bionano N/A 646.50x 1.4 GiB
Arima 98.51 Gbp 98.51x 67.9 GiB
Bases and Coverage are approximate.
Coverage based on genome size 1.00 Gbp.
Last upload on 19 April 2021.
Assemblies
Individual 1 Primary Assembly
Version assembly_curated from 25 May 2021
bTroSur1.pri.cur.20210525.fasta.gz (338.9 MiB)

Quality: 22.5 errors/Mb (QV=46.48)

Contigs Scaffolds
NG LG Len LG Len
10 2 38.58 Mbp 0 222.21 Mbp
20 5 33.16 Mbp 0 222.21 Mbp
30 8 26.86 Mbp 1 127.11 Mbp
40 12 22.53 Mbp 2 100.50 Mbp
50 17 17.93 Mbp 3 87.90 Mbp
60 23 15.32 Mbp 4 82.62 Mbp
70 31 11.71 Mbp 5 82.43 Mbp
80 41 8.92 Mbp 7 47.45 Mbp
90 53 7.33 Mbp 11 22.25 Mbp
100 70 4.55 Mbp 16 17.58 Mbp
1.155x 434 1.16 Gbp 181 1.17 Gbp
NG based on genome size 1.00 Gbp.
Individual 1 Alternate Assembly
Version assembly_curated from 25 May 2021
bTroSur1.alt.cur.20210525.fasta.gz (292.8 MiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 19 3.79 Mbp 19 3.79 Mbp
20 49 2.95 Mbp 49 2.95 Mbp
30 86 2.42 Mbp 86 2.42 Mbp
40 135 1.84 Mbp 135 1.84 Mbp
50 195 1.47 Mbp 195 1.47 Mbp
60 272 1.14 Mbp 272 1.14 Mbp
70 372 0.88 Mbp 371 0.88 Mbp
80 505 0.64 Mbp 504 0.64 Mbp
90 711 348.10 Kbp 709 351.43 Kbp
100 0 0
0.997x 1552 1.00 Gbp 1535 1.00 Gbp
NG based on genome size 1.00 Gbp.
Individual 1 Mitochondrial Assembly
Version assembly_MT_rockefeller from 21 January 2021
bTroSur1.MT.20210121.fasta.gz (5.2 KiB)

Quality: not computed
Assembly Metadata
assembly_vgp_standard_1.6/bTroSur1.yaml (view)
species: Trogon surrucura
specimen: bTroSur1
projects:
  - vgp
primary: s3://genomeark/species/Trogon_surrucura/bTroSur1/assembly_vgp_standard_1.6/bTroSur1.pri.asm.20210407.fasta.gz
haplotigs: s3://genomeark/species/Trogon_surrucura/bTroSur1/assembly_vgp_standard_1.6/bTroSur1.alt.asm.20210407.fasta.gz
mito: s3://genomeark/species/Trogon_surrucura/bTroSur1/assembly_MT_rockefeller/bTroSur1.MT.20210121.fasta.gz
bTroSur1_metadata.yml (view)
samples:
- Sample Source: Smithsonian
  VGP_Id: bTroSur1
  birth_date: ''
  collected_by: Banin  D. A.
  collection_date: 10/29/1995
  common_name: Suruca trogon
  description: 'Family #: 2010; Family: Trogonidae; State/Province: Misiones; Precise
    Location: Posadas  45 km N  80 km E; Latitude: 26 57 19 S; Longitude: 55 05 16
    W; Elevation: 250 m; Field #(s): BKS 2847; Tissue #: B05987; Preparation: Skeleton:
    Whole; Weight: 69.8 g; Preparator: Brian K. Schmidt BKS 2847; Fat: little; Bursa:
    none; Reproduction: Ovary: 12 x 6 mm  largest ova 2 mm; Oviduct: 5 mm  at cloaca;
    Molt: whole bird: none; Habitat: mosaic of humid forest with second growth at
    edges ; Status: Collection'
  dev_stage: ''
  geo_loc_name: Argentina
  individual_id: ''
  lat_lon: 26 57 19 S; 55 05 16 W
  scientific_name: Trogon surrucura
  sex: female
  store_cond: -80C
  taxon_Id: '297711'
  tissue: Unknown
  treatment: ''
  tube_id: bTroSur1.Uk1
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.