Pan troglodytes

chimpanzee

Included in the VGP and T2T.


metadata.yaml (view) (edit on github)
CC BY-SA 2.0 Bernard Dupont (wikipedia)
Raw Data by Technology
Datatype Individual Bases Coverage Bytes Access
PacBio CLR mPanTro1 398.91 Gbp 110.39x 1.4 TiB
PacBio HiFi (subreads) mPanTro1 4884.92 Gbp 1351.77x 8.3 TiB
mPanTro3 3799.28 Gbp 1051.35x 6.7 TiB
PacBio HiFi (.fq, Q≥20) mPanTro1 139.53 Gbp 38.61x 95.5 GiB
PacBio HiFi (.fq) mPanTro1 229.20 Gbp 63.43x 178.5 GiB
mPanTro3 429.26 Gbp 118.79x 312.6 GiB
PacBio HiFi (.bam) mPanTro1 424.07 Gbp 117.35x 0.9 TiB
mPanTro3 734.38 Gbp 203.22x 775.5 GiB
Oxford Nanopore Simplex mPanTro1 327.43 Gbp 90.61x 253.7 GiB
mPanTro3 794.25 Gbp 219.79x 646.4 GiB
10x mPanTro1 248.16 Gbp 68.67x 153.5 GiB
Bionano mPanTro1 N/A 226.94x 735.6 MiB
Dovetail Genomics mPanTro3 190.56 Gbp 52.73x 94.9 GiB
Illumina mPanTro3 176.42 Gbp 48.82x 89.8 GiB
Bases and Coverage are approximate.
Coverage based on genome size 3.61 Gbp.
Last upload on 19 December 2023.
Raw Data by Individual
Individual Datatype Bases Coverage Bytes Access
mPanTro1 PacBio CLR 398.91 Gbp 110.39x 1.4 TiB
PacBio HiFi (subreads) 4884.92 Gbp 1351.77x 8.3 TiB
PacBio HiFi (.fq, Q≥20) 139.53 Gbp 38.61x 95.5 GiB
PacBio HiFi (.fq) 229.20 Gbp 63.43x 178.5 GiB
PacBio HiFi (.bam) 424.07 Gbp 117.35x 0.9 TiB
Oxford Nanopore Simplex 327.43 Gbp 90.61x 253.7 GiB
10x 248.16 Gbp 68.67x 153.5 GiB
Bionano N/A 226.94x 735.6 MiB
mPanTro3 PacBio HiFi (subreads) 3799.28 Gbp 1051.35x 6.7 TiB
PacBio HiFi (.fq) 429.26 Gbp 118.79x 312.6 GiB
PacBio HiFi (.bam) 734.38 Gbp 203.22x 775.5 GiB
Oxford Nanopore Simplex 794.25 Gbp 219.79x 646.4 GiB
Dovetail Genomics 190.56 Gbp 52.73x 94.9 GiB
Illumina 176.42 Gbp 48.82x 89.8 GiB
Bases and Coverage are approximate.
Coverage based on genome size 3.61 Gbp.
Last upload on 19 December 2023.
Assemblies
Individual 1 Mitochondrial Assembly
Version assembly_MT_rockefeller from 25 June 2020
mPanTro1.MT.20200625.fasta.gz (4.9 KiB)

Quality: not computed

Individual 3 Diploid Assembly
Version assembly_curated from 22 November 2023
mPanTro3.dip.cur.20231122.fasta.gz (1.7 GiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 2 231.30 Mbp 2 231.30 Mbp
20 4 200.34 Mbp 4 200.34 Mbp
30 6 191.67 Mbp 6 191.67 Mbp
40 8 180.08 Mbp 8 180.08 Mbp
50 10 178.96 Mbp 10 178.96 Mbp
60 12 168.85 Mbp 12 168.85 Mbp
70 14 155.69 Mbp 14 155.69 Mbp
80 16 147.43 Mbp 16 147.43 Mbp
90 19 140.84 Mbp 19 140.84 Mbp
100 21 138.75 Mbp 21 138.75 Mbp
1.706x 58 6.17 Gbp 48 6.18 Gbp
NG based on genome size 3.61 Gbp.
Individual 3 Primary Assembly
Version assembly_curated from 22 November 2023
mPanTro3.pri.cur.20231122.fasta.gz (885.3 MiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 2 201.58 Mbp 2 201.58 Mbp
20 4 183.32 Mbp 4 183.32 Mbp
30 6 174.65 Mbp 6 174.65 Mbp
40 8 153.90 Mbp 8 153.90 Mbp
50 11 140.16 Mbp 11 140.16 Mbp
60 14 118.86 Mbp 14 120.15 Mbp
70 17 99.60 Mbp 17 99.60 Mbp
80 21 78.12 Mbp 21 78.12 Mbp
90 0 0
100 0 0
0.878x 30 3.17 Gbp 25 3.18 Gbp
NG based on genome size 3.61 Gbp.
Individual 3 Alternate Assembly
Version assembly_curated from 22 November 2023
mPanTro3.alt.cur.20231122.fasta.gz (832.7 MiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 2 200.34 Mbp 2 200.34 Mbp
20 4 180.08 Mbp 4 180.08 Mbp
30 6 168.85 Mbp 6 168.85 Mbp
40 8 147.43 Mbp 8 147.43 Mbp
50 11 136.44 Mbp 11 136.44 Mbp
60 14 115.41 Mbp 14 118.00 Mbp
70 17 97.71 Mbp 17 97.71 Mbp
80 22 52.30 Mbp 21 73.83 Mbp
90 0 0
100 0 0
0.828x 28 2.99 Gbp 23 3.00 Gbp
NG based on genome size 3.61 Gbp.
Individual 3 Haplotype 1 Assembly
Version assembly_curated from 22 November 2023
mPanTro3.hap1.cur.20231122.fasta.gz (876.0 MiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 2 201.58 Mbp 2 201.58 Mbp
20 4 183.32 Mbp 4 183.32 Mbp
30 6 174.65 Mbp 6 174.65 Mbp
40 8 153.90 Mbp 8 153.90 Mbp
50 11 140.16 Mbp 11 140.16 Mbp
60 14 118.86 Mbp 14 120.15 Mbp
70 17 99.60 Mbp 17 99.60 Mbp
80 21 78.12 Mbp 21 78.12 Mbp
90 0 0
100 0 0
0.868x 29 3.14 Gbp 24 3.14 Gbp
NG based on genome size 3.61 Gbp.
Individual 3 Haplotype 2 Assembly
Version assembly_curated from 22 November 2023
mPanTro3.hap2.cur.20231122.fasta.gz (842.1 MiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 2 200.34 Mbp 2 200.34 Mbp
20 4 180.08 Mbp 4 180.08 Mbp
30 6 168.85 Mbp 6 168.85 Mbp
40 8 147.43 Mbp 8 147.43 Mbp
50 11 136.44 Mbp 11 136.44 Mbp
60 14 115.41 Mbp 14 118.00 Mbp
70 17 97.71 Mbp 17 97.71 Mbp
80 22 52.30 Mbp 21 73.83 Mbp
90 0 0
100 0 0
0.838x 29 3.03 Gbp 24 3.03 Gbp
NG based on genome size 3.61 Gbp.
Individual 3 Mitochondrial Assembly
Version assembly_curated from 22 November 2023
mPanTro3.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.