Pongo abelii

Sumatran orangutan

Included in the T2T.

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


metadata.yaml (view) (edit on github)
species:
  short_name: mPonAbe
  name: Pongo abelii
  common_name: Sumatran orangutan
  taxon_id: 9601
  order:
    name: Primates
  family:
    name: Hominidae
  individuals:
  -
      short_name: mPonAbe1
      name: null
      biosample_id: SAMN10521808
      strain: null
      subspecies: null
      alt_ids:
      - GM06213
      - AG06213
      - AG06123_PAB
      sex: male
      description: null
      provider: Laura Carrel (The Pennsylvania State University), originally acquired from Coriell
      father: null
      mother: null
  -
      short_name: mPonAbe2
      name: null
      biosample_id: null
      strain: null
      alt_ids:
      - PAB_1991-51
      - Ppyab 1991-51
      - 1991-51
      sex: male
      description: null
      provider: Andrew Cartoceti (Smithsonian Institution)
      mother: null
      father: null
      samples:
      -
         sample_id: mPonAbe2.testis1
         tissue: testis
         dev_stage: adult
         age: 31
         sample_biosample_id: SAMN13178754
  -
      short_name: mPonAbe3
      name: Susie
      biosample_id: SAMN06275555
      strain: null
      alt_ids:
      - Susie_PAB
      - 1044
      sex: female
      description: null
      provider: Dr. Oliver Ryder (Institute for Conservation Research, San Diego Zoo)
      mother: null
      father: null
  genome_size: 3579480000
  genome_size_method: GoaT ancestral inferred
  project: [ t2t ]
CC BY-SA 3.0 Greg Hume (Wikimedia)
Raw Data by Technology
Datatype Individual Bases Coverage Bytes Access
PacBio HiFi (subreads) mPonAbe1 5011.07 Gbp 1399.94x 9.2 TiB
PacBio HiFi (.fq) mPonAbe1 641.31 Gbp 179.16x 468.1 GiB
PacBio HiFi (.bam) mPonAbe1 438.80 Gbp 122.59x 1.2 TiB
Oxford Nanopore Simplex mPonAbe1 567.29 Gbp 158.48x 469.0 GiB
Dovetail Genomics mPonAbe1 112.53 Gbp 31.44x 56.9 GiB
Illumina mPonAbe1 223.75 Gbp 62.51x 112.5 GiB
Bases and Coverage are approximate.
Coverage based on genome size 3.58 Gbp.
Last upload on 1 November 2023.
Raw Data by Individual
Individual Datatype Bases Coverage Bytes Access
mPonAbe1 PacBio HiFi (subreads) 5011.07 Gbp 1399.94x 9.2 TiB
PacBio HiFi (.fq) 641.31 Gbp 179.16x 468.1 GiB
PacBio HiFi (.bam) 438.80 Gbp 122.59x 1.2 TiB
Oxford Nanopore Simplex 567.29 Gbp 158.48x 469.0 GiB
Dovetail Genomics 112.53 Gbp 31.44x 56.9 GiB
Illumina 223.75 Gbp 62.51x 112.5 GiB
Bases and Coverage are approximate.
Coverage based on genome size 3.58 Gbp.
Last upload on 1 November 2023.
Assemblies
Individual 1 Diploid Assembly
Version assembly_curated from 5 December 2023
mPonAbe1.dip.cur.20231205.fasta.gz (1.5 GiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 2 233.65 Mbp 2 233.80 Mbp
20 4 212.22 Mbp 4 212.22 Mbp
30 5 209.61 Mbp 5 209.61 Mbp
40 7 190.38 Mbp 7 190.38 Mbp
50 9 172.61 Mbp 9 172.61 Mbp
60 11 165.38 Mbp 11 165.38 Mbp
70 13 161.63 Mbp 13 161.63 Mbp
80 16 146.20 Mbp 16 146.20 Mbp
90 18 140.85 Mbp 18 140.85 Mbp
100 21 132.28 Mbp 21 137.95 Mbp
1.745x 98 6.25 Gbp 77 6.26 Gbp
NG based on genome size 3.58 Gbp.
Individual 1 Primary Assembly
Version assembly_curated from 5 December 2023
mPonAbe1.pri.cur.20231205.fasta.gz (809.7 MiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 2 212.92 Mbp 2 212.92 Mbp
20 4 190.38 Mbp 4 190.38 Mbp
30 6 162.59 Mbp 6 162.59 Mbp
40 8 156.97 Mbp 8 156.97 Mbp
50 11 138.47 Mbp 11 138.47 Mbp
60 13 129.81 Mbp 13 132.28 Mbp
70 16 109.57 Mbp 16 111.74 Mbp
80 20 84.05 Mbp 20 89.55 Mbp
90 25 54.96 Mbp 25 57.14 Mbp
100 0 0
0.908x 40 3.25 Gbp 29 3.26 Gbp
NG based on genome size 3.58 Gbp.
Individual 1 Alternate Assembly
Version assembly_curated from 5 December 2023
mPonAbe1.alt.cur.20231205.fasta.gz (749.2 MiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 2 212.22 Mbp 2 212.22 Mbp
20 4 189.72 Mbp 4 189.72 Mbp
30 6 165.38 Mbp 6 165.38 Mbp
40 8 143.46 Mbp 8 145.71 Mbp
50 11 129.47 Mbp 11 132.23 Mbp
60 14 102.46 Mbp 13 124.96 Mbp
70 17 90.13 Mbp 17 101.03 Mbp
80 22 51.98 Mbp 21 68.78 Mbp
90 0 0
100 0 0
0.836x 58 2.99 Gbp 48 3.00 Gbp
NG based on genome size 3.58 Gbp.
Individual 1 Haplotype 1 Assembly
Version assembly_curated from 5 December 2023
mPonAbe1.hap1.cur.20231205.fasta.gz (795.5 MiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 2 212.92 Mbp 2 212.92 Mbp
20 4 190.38 Mbp 4 190.38 Mbp
30 6 162.59 Mbp 6 162.59 Mbp
40 8 156.97 Mbp 8 156.97 Mbp
50 11 138.47 Mbp 11 138.47 Mbp
60 13 129.81 Mbp 13 132.28 Mbp
70 16 109.57 Mbp 16 111.74 Mbp
80 20 84.05 Mbp 20 89.55 Mbp
90 0 0
100 0 0
0.890x 39 3.18 Gbp 28 3.19 Gbp
NG based on genome size 3.58 Gbp.
Individual 1 Haplotype 2 Assembly
Version assembly_curated from 5 December 2023
mPonAbe1.hap2.cur.20231205.fasta.gz (763.4 MiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 2 212.22 Mbp 2 212.22 Mbp
20 4 189.72 Mbp 4 189.72 Mbp
30 6 165.38 Mbp 6 165.38 Mbp
40 8 143.46 Mbp 8 145.71 Mbp
50 11 129.47 Mbp 11 132.23 Mbp
60 14 102.46 Mbp 13 124.96 Mbp
70 17 90.13 Mbp 17 101.03 Mbp
80 22 67.83 Mbp 21 68.78 Mbp
90 0 0
100 0 0
0.855x 59 3.06 Gbp 49 3.07 Gbp
NG based on genome size 3.58 Gbp.
Individual 1 Mitochondrial Assembly
Version assembly_curated from 22 November 2023
mPonAbe1.MT.cur.20231122.fasta.gz (5.2 KiB)

Quality: not computed
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.