Theristicus caerulescens

plumbeous ibis

Included in the VGP.

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


Resource Primary Assembly Alternate Assembly
GenBank bTheCae1: GCA_020745775.1 bTheCae1: GCA_020745805.1
ENA bTheCae1: GCA_020745775.1 bTheCae1: GCA_020745805.1
UCSC Genome Browser bTheCae1: GCA_020745775.1 bTheCae1: GCA_020745805.1

metadata.yaml (view) (edit on github)
species:
  short_name: bTheCae
  name: Theristicus caerulescens
  taxon_id: 1118847
  common_name: plumbeous ibis
  order:
    name: Pelicaniformes
  family:
    name: Threskiornithidae
  individuals:
    - short_name: bTheCae1
  genome_size: 1000000000
  genome_size_method:
  project: [ vgp ]
CC BY-SA 2.0 Bernard DUPONT (flickr)
Raw Data by Technology
Datatype Individual Bases Coverage Bytes Access
PacBio CLR bTheCae1 160.49 Gbp 160.49x 284.3 GiB
10x bTheCae1 140.72 Gbp 140.72x 69.4 GiB
Bionano bTheCae1 N/A 524.88x 1.2 GiB
Arima bTheCae1 250.14 Gbp 250.14x 160.1 GiB
Bases and Coverage are approximate.
Coverage based on genome size 1.00 Gbp.
Last upload on 26 January 2021.
Raw Data by Individual
Individual Datatype Bases Coverage Bytes Access
bTheCae1 PacBio CLR 160.49 Gbp 160.49x 284.3 GiB
10x 140.72 Gbp 140.72x 69.4 GiB
Bionano N/A 524.88x 1.2 GiB
Arima 250.14 Gbp 250.14x 160.1 GiB
Bases and Coverage are approximate.
Coverage based on genome size 1.00 Gbp.
Last upload on 26 January 2021.
Assemblies
Individual 1 Primary Assembly
Version assembly_curated from 25 May 2021
bTheCae1.pri.cur.20210525.fasta.gz (351.9 MiB)

Quality: 33.7 errors/Mb (QV=44.72)

Contigs Scaffolds
NG LG Len LG Len
10 0 106.66 Mbp 0 168.28 Mbp
20 1 103.95 Mbp 1 133.04 Mbp
30 3 62.37 Mbp 1 133.04 Mbp
40 5 44.65 Mbp 2 128.21 Mbp
50 7 41.77 Mbp 3 128.01 Mbp
60 9 37.10 Mbp 4 101.37 Mbp
70 13 27.55 Mbp 5 92.93 Mbp
80 17 20.81 Mbp 6 84.85 Mbp
90 22 13.59 Mbp 7 72.38 Mbp
100 30 11.40 Mbp 9 50.21 Mbp
1.201x 191 1.20 Gbp 87 1.20 Gbp
NG based on genome size 1.00 Gbp.
Individual 1 Alternate Assembly
Version assembly_curated from 25 May 2021
bTheCae1.alt.cur.20210525.fasta.gz (305.3 MiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 7 11.24 Mbp 7 11.24 Mbp
20 17 9.26 Mbp 17 9.26 Mbp
30 29 7.73 Mbp 29 7.73 Mbp
40 44 5.82 Mbp 43 5.90 Mbp
50 62 4.88 Mbp 62 4.88 Mbp
60 85 4.13 Mbp 84 4.19 Mbp
70 113 3.09 Mbp 113 3.09 Mbp
80 154 2.05 Mbp 154 2.05 Mbp
90 216 1.25 Mbp 215 1.26 Mbp
100 363 285.09 Kbp 362 285.09 Kbp
1.041x 753 1.04 Gbp 749 1.04 Gbp
NG based on genome size 1.00 Gbp.
Individual 1 Mitochondrial Assembly
Version assembly_MT_rockefeller from 20 January 2021
bTheCae1.MT.20210120.fasta.gz (5.2 KiB)

Quality: not computed
Assembly Metadata
assembly_vgp_standard_1.6/bTheCae1.yaml (view)
species: Theristicus caerulescens
specimen: bTheCae1
projects:
  - vgp
primary: s3://genomeark/species/Theristicus_caerulescens/bTheCae1/assembly_vgp_standard_1.6/bTheCae1.pri.asm.20210407.fasta.gz
haplotigs: s3://genomeark/species/Theristicus_caerulescens/bTheCae1/assembly_vgp_standard_1.6/bTheCae1.alt.asm.20210407.fasta.gz
mito: s3://genomeark/species/Theristicus_caerulescens/bTheCae1/assembly_MT_rockefeller/bTheCae1.MT.20210120.fasta.gz
bTheCae1_metadata.yml (view)
samples:
- Sample Source: Smithsonian
  VGP_Id: bTheCae1
  birth_date: ''
  collected_by: Milensky  C. M.
  collection_date: 10/26/2005
  common_name: plumbeous ibis
  description: 'Family #: 0750; Family: Threskiornithidae; Subfamily: Threskiornithinae;
    State/Province: Rocha; Precise Location: 18 de Julio  19 km W  at Estancia La
    Canada; Latitude: 33 44 31 S; Longitude: 53 44 46 W; Elevation: 50 m; Field #(s):
    CAG 1760; 37; Tissue #: B20749; Stage: Chick; Preparation: Skin: Whole; Weight:
    54.3 g; Preparator: Christina A. Gebhard CAG 1760; Fat: moderate; Reproduction:
    Ovary: 3 x 1 mm  smooth yellowish; Softparts: iris: gray brown; tarsi: orangish
    tan; bill: black with creamish tip and egg tooth; Collection Method: shot; Remarks:
    field notes: Egg shell was still in nest and collected. Two other unhatched eggs
    were in the nest and collected. Photos of the nest were taken. One adult was sitting
    on the nest when collected.; Status: Collection'
  dev_stage: juvenile
  geo_loc_name: Uruguay
  individual_id: ''
  lat_lon: 33 44 31 S; 53 44 46 W
  scientific_name: Theristicus caerulescens
  sex: female
  store_cond: -80C
  taxon_Id: '1118847'
  tissue: Unknown
  treatment: ''
  tube_id: bTheCae1.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.