Pongo_pygmaeus

Pongo pygmaeus

Bornean orangutan

Included in the T2T.

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

metadata.yaml (view) (edit on github)
species: short_name: mPonPyg name: Pongo pygmaeus common_name: Bornean orangutan taxon_id: 9600 order: name: Primates family: name: Hominidae individuals: - short_name: mPonPyg2 name: null biosample_id: SAMN10521809 strain: null subspecies: null alt_ids: - AG05252 - AG05252_PPY sex: male description: null provider: Coriell father: null mother: null - short_name: mPonPyg3 subspecies: name: Pongo pygmaeus pygmaeus common_name: Northwest Bornean orangutan taxon_id: 9602 name: null biosample_id: null strain: null alt_ids: - PPY_3405 - Ppypy 3405 - 3405 sex: male description: null provider: Oliver Ryder (San Diego Zoo Wildlife Alliance) mother: null father: null samples: - sample_id: mPonPyg3.testis1 tissue: testis dev_stage: adult sample_biosample_id: SAMN13178639 genome_size: 3579480000 genome_size_method: GoaT Fuelgen Densitometry/Flow Cytometry project: [ t2t ]

species:
  short_name: mPonPyg
  name: Pongo pygmaeus
  common_name: Bornean orangutan
  taxon_id: 9600
  order:
    name: Primates
  family:
    name: Hominidae
  individuals:
  -
      short_name: mPonPyg2
      name: null
      biosample_id: SAMN10521809
      strain: null
      subspecies: null
      alt_ids:
      - AG05252
      - AG05252_PPY
      sex: male
      description: null
      provider: Coriell
      father: null
      mother: null
  -
      short_name: mPonPyg3
      subspecies:
        name: Pongo pygmaeus pygmaeus
        common_name: Northwest Bornean orangutan
        taxon_id: 9602
      name: null
      biosample_id: null
      strain: null
      alt_ids:
      - PPY_3405
      - Ppypy 3405
      - 3405
      sex: male
      description: null
      provider: Oliver Ryder (San Diego Zoo Wildlife Alliance)
      mother: null
      father: null
      samples:
      -
         sample_id: mPonPyg3.testis1
         tissue: testis
         dev_stage: adult
         sample_biosample_id: SAMN13178639
  genome_size: 3579480000
  genome_size_method: GoaT Fuelgen Densitometry/Flow Cytometry
  project: [ t2t ]

CC BY-NC-SA 2.0 Joachim S. Müller (flickr)

Datatype	Individual	Bases	Coverage	Bytes
PacBio HiFi (subreads)	mPonPyg2	3481.77 Gbp	972.70x	6.4 TiB
PacBio HiFi (.fq)	mPonPyg2	384.41 Gbp	107.39x	320.0 GiB
PacBio HiFi (.bam)	mPonPyg2	648.93 Gbp	181.29x	707.3 GiB
Oxford Nanopore Simplex	mPonPyg2	1307.07 Gbp	365.16x	1.0 TiB
Dovetail Genomics	mPonPyg2	170.10 Gbp	47.52x	87.2 GiB
Illumina	mPonPyg2	166.03 Gbp	46.38x	83.3 GiB

Bases and Coverage are approximate.
Coverage based on genome size 3.58 Gbp.
Last upload on 29 October 2023.

Individual	Datatype	Bases	Coverage	Bytes
mPonPyg2	PacBio HiFi (subreads)	3481.77 Gbp	972.70x	6.4 TiB
	PacBio HiFi (.fq)	384.41 Gbp	107.39x	320.0 GiB
	PacBio HiFi (.bam)	648.93 Gbp	181.29x	707.3 GiB
	Oxford Nanopore Simplex	1307.07 Gbp	365.16x	1.0 TiB
	Dovetail Genomics	170.10 Gbp	47.52x	87.2 GiB
	Illumina	166.03 Gbp	46.38x	83.3 GiB

Bases and Coverage are approximate.
Coverage based on genome size 3.58 Gbp.
Last upload on 29 October 2023.

Individual 2 Diploid Assembly
Version assembly_curated from 22 November 2023
mPonPyg2.dip.cur.20231122.fasta.gz (1.7 GiB)

Quality: not computed

	Contigs		Scaffolds
NG	LG	Len	LG	Len
10	2	230.81 Mbp	2	230.81 Mbp
20	4	209.25 Mbp	4	209.25 Mbp
30	5	203.83 Mbp	5	203.83 Mbp
40	7	186.35 Mbp	7	186.35 Mbp
50	9	172.53 Mbp	9	172.53 Mbp
60	11	160.97 Mbp	11	160.97 Mbp
70	14	158.53 Mbp	14	158.53 Mbp
80	16	140.59 Mbp	16	143.26 Mbp
90	19	137.91 Mbp	18	140.58 Mbp
100	21	135.49 Mbp	21	137.70 Mbp
1.735x	76	6.21 Gbp	58	6.23 Gbp

NG based on genome size 3.58 Gbp.

Individual 2 Primary Assembly
Version assembly_curated from 22 November 2023
mPonPyg2.pri.cur.20231122.fasta.gz (0.9 GiB)

Quality: not computed

	Contigs		Scaffolds
NG	LG	Len	LG	Len
10	2	209.44 Mbp	2	209.44 Mbp
20	4	186.35 Mbp	4	186.35 Mbp
30	6	160.97 Mbp	6	160.97 Mbp
40	8	158.15 Mbp	8	158.15 Mbp
50	11	137.03 Mbp	11	137.03 Mbp
60	13	131.76 Mbp	13	132.18 Mbp
70	16	104.54 Mbp	16	107.89 Mbp
80	20	87.43 Mbp	20	87.43 Mbp
90	0		0
100	0		0
0.898x	33	3.21 Gbp	25	3.22 Gbp

NG based on genome size 3.58 Gbp.

Individual 2 Alternate Assembly
Version assembly_curated from 22 November 2023
mPonPyg2.alt.cur.20231122.fasta.gz (845.4 MiB)

Quality: not computed

	Contigs		Scaffolds
NG	LG	Len	LG	Len
10	2	209.25 Mbp	2	209.25 Mbp
20	4	183.84 Mbp	4	183.84 Mbp
30	6	159.28 Mbp	6	159.28 Mbp
40	8	139.77 Mbp	8	141.98 Mbp
50	11	135.21 Mbp	11	137.70 Mbp
60	14	107.22 Mbp	14	121.93 Mbp
70	17	95.11 Mbp	17	98.35 Mbp
80	22	56.90 Mbp	21	62.95 Mbp
90	0		0
100	0		0
0.838x	43	3.00 Gbp	33	3.01 Gbp

NG based on genome size 3.58 Gbp.

Individual 2 Haplotype 1 Assembly
Version assembly_curated from 22 November 2023
mPonPyg2.hap1.cur.20231122.fasta.gz (891.9 MiB)

Quality: not computed

	Contigs		Scaffolds
NG	LG	Len	LG	Len
10	2	209.44 Mbp	2	209.44 Mbp
20	4	186.35 Mbp	4	186.35 Mbp
30	6	160.97 Mbp	6	160.97 Mbp
40	8	158.15 Mbp	8	158.15 Mbp
50	11	137.03 Mbp	11	137.03 Mbp
60	13	131.76 Mbp	13	132.18 Mbp
70	16	104.54 Mbp	16	107.89 Mbp
80	20	87.43 Mbp	20	87.43 Mbp
90	0		0
100	0		0
0.884x	32	3.16 Gbp	24	3.17 Gbp

NG based on genome size 3.58 Gbp.

Individual 2 Haplotype 2 Assembly
Version assembly_curated from 22 November 2023
mPonPyg2.hap2.cur.20231122.fasta.gz (858.1 MiB)

Quality: not computed

	Contigs		Scaffolds
NG	LG	Len	LG	Len
10	2	209.25 Mbp	2	209.25 Mbp
20	4	183.84 Mbp	4	183.84 Mbp
30	6	159.28 Mbp	6	159.28 Mbp
40	8	139.77 Mbp	8	141.98 Mbp
50	11	135.21 Mbp	11	137.70 Mbp
60	14	107.22 Mbp	14	121.93 Mbp
70	17	95.11 Mbp	17	98.35 Mbp
80	22	56.90 Mbp	21	62.95 Mbp
90	0		0
100	0		0
0.851x	44	3.05 Gbp	34	3.06 Gbp

NG based on genome size 3.58 Gbp.

Individual 2 Mitochondrial Assembly
Version assembly_curated from 22 November 2023
mPonPyg2.MT.cur.20231122.fasta.gz (5.3 KiB)

Quality: not computed

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.