Description

This track represents copy number estimates. Copy number is estimated over 500 bp windows of uniquely mappable sequence. Sequences are colored from cold to hot (0 - 120+) and exact copy can be found by clicking on the region of interest.

Code Availability

GitHub

Copy Number Key

Copy numberColor
0
■
1
■
2
■
3
■
4
■
5
■
6
■
7
■
8
■
9
■
10
■
20
■
30
■
40
■
50
■
60
■
70
■
80
■
90
■
100
■
110
■
120
■

Credits

Please feel free to contact William Harvey or Mitchell Vollger with any questions and/or concerns regarding this track.

References

Bailey JA, Gu Z, Clark RA, Reinert K, Samonte RV, Schwartz S, Adams MD, Myers EW, Li PW, Eichler EE. Recent segmental duplications in the human genome. Science 2002

Pendleton AL, Shen F, Taravella AM, Emery S, Veeramah KR, Boyko AR, Kidd JM. Comparison of village dog and wolf genomes highlights the role of the neural crest in dog domestication. BMC Biol. 2018

Sudmant PH, Mallick S, Nelson BJ, Hormozdiari F, Krumm N, Huddleston J, et al. Global diversity, population stratification, and selection of human copy-number variation. Science. 2015

Sudmant PH, Kitzman JO, Antonacci F, Alkan C, Malig M, Tsalenko A, et al. Diversity of human copy number. Science. 2010

Sample table

SampleRead file
CHM13_kmer/net/eichler/vol26/projects/chm13_t2t/nobackups/wssd/v1.0/kmer/chm13_v1.1_noY_kmer.fasta.gz
HG00438/net/eichler/vol26/projects/1kg_high_coverage/nobackups/data/Illumina/cram/HG00438.final.cram
HG00621/net/eichler/vol26/projects/1kg_high_coverage/nobackups/data/Illumina/cram/HG00621.final.cram
HG00673/net/eichler/vol26/projects/1kg_high_coverage/nobackups/data/Illumina/cram/HG00673.final.cram
HG00733/net/eichler/vol26/projects/1kg_high_coverage/nobackups/data/Illumina/cram/HG00733.final.cram
HG00735/net/eichler/vol26/projects/1kg_high_coverage/nobackups/data/Illumina/cram/HG00735.final.cram
HG00741/net/eichler/vol26/projects/1kg_high_coverage/nobackups/data/Illumina/cram/HG00741.final.cram
HG01071/net/eichler/vol26/projects/1kg_high_coverage/nobackups/data/Illumina/cram/HG01071.final.cram
HG01106/net/eichler/vol26/projects/1kg_high_coverage/nobackups/data/Illumina/cram/HG01106.final.cram
HG01109/net/eichler/vol26/projects/1kg_high_coverage/nobackups/data/Illumina/cram/HG01109.final.cram
HG01175/net/eichler/vol26/projects/1kg_high_coverage/nobackups/data/Illumina/cram/HG01175.final.cram
HG01243/net/eichler/vol26/projects/1kg_high_coverage/nobackups/data/Illumina/cram/HG01243.final.cram
HG01258/net/eichler/vol26/projects/1kg_high_coverage/nobackups/data/Illumina/cram/HG01258.final.cram
HG01358/net/eichler/vol26/projects/1kg_high_coverage/nobackups/data/Illumina/cram/HG01358.final.cram
HG01361/net/eichler/vol26/projects/1kg_high_coverage/nobackups/data/Illumina/cram/HG01361.final.cram
HG01891/net/eichler/vol26/projects/1kg_high_coverage/nobackups/data/Illumina/cram/HG01891.final.cram
HG01928/net/eichler/vol26/projects/1kg_high_coverage/nobackups/data/Illumina/cram/HG01928.final.cram
HG01952/net/eichler/vol26/projects/1kg_high_coverage/nobackups/data/Illumina/cram/HG01952.final.cram
HG01978/net/eichler/vol26/projects/1kg_high_coverage/nobackups/data/Illumina/cram/HG01978.final.cram
HG02055/net/eichler/vol26/projects/1kg_high_coverage/nobackups/data/Illumina/cram/HG02055.final.cram
HG02080/net/eichler/vol26/projects/1kg_high_coverage/nobackups/data/Illumina/cram/HG02080.final.cram
HG02145/net/eichler/vol26/projects/1kg_high_coverage/nobackups/data/Illumina/cram/HG02145.final.cram
HG02148/net/eichler/vol26/projects/1kg_high_coverage/nobackups/data/Illumina/cram/HG02148.final.cram
HG02257/net/eichler/vol26/projects/1kg_high_coverage/nobackups/data/Illumina/cram/HG02257.final.cram
HG02572/net/eichler/vol26/projects/1kg_high_coverage/nobackups/data/Illumina/cram/HG02572.final.cram
HG02622/net/eichler/vol26/projects/1kg_high_coverage/nobackups/data/Illumina/cram/HG02622.final.cram
HG02630/net/eichler/vol26/projects/1kg_high_coverage/nobackups/data/Illumina/cram/HG02630.final.cram
HG02717/net/eichler/vol26/projects/1kg_high_coverage/nobackups/data/Illumina/cram/HG02717.final.cram
HG02723/net/eichler/vol26/projects/1kg_high_coverage/nobackups/data/Illumina/cram/HG02723.final.cram
HG02818/net/eichler/vol26/projects/1kg_high_coverage/nobackups/data/Illumina/cram/HG02818.final.cram
HG02886/net/eichler/vol26/projects/1kg_high_coverage/nobackups/data/Illumina/cram/HG02886.final.cram
HG03098/net/eichler/vol26/projects/1kg_high_coverage/nobackups/data/Illumina/cram/HG03098.final.cram
HG03453/net/eichler/vol26/projects/1kg_high_coverage/nobackups/data/Illumina/cram/HG03453.final.cram
HG03486/net/eichler/vol26/projects/1kg_high_coverage/nobackups/data/Illumina/cram/HG03486.final.cram
HG03492/net/eichler/vol26/projects/1kg_high_coverage/nobackups/data/Illumina/cram/HG03492.final.cram
HG03516/net/eichler/vol26/projects/1kg_high_coverage/nobackups/data/Illumina/cram/HG03516.final.cram
HG03540/net/eichler/vol26/projects/1kg_high_coverage/nobackups/data/Illumina/cram/HG03540.final.cram
HG03579/net/eichler/vol26/projects/1kg_high_coverage/nobackups/data/Illumina/cram/HG03579.final.cram
NA18906/net/eichler/vol26/projects/1kg_high_coverage/nobackups/data/Illumina/cram/NA18906.final.cram
NA19240/net/eichler/vol26/projects/1kg_high_coverage/nobackups/data/Illumina/cram/NA19240.final.cram
NA20129/net/eichler/vol26/projects/1kg_high_coverage/nobackups/data/Illumina/cram/NA20129.final.cram