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SGDP copy number subset Track Settings   SGDP copy number estimates subset   (All Variation and Repeats tracks) Display mode:  hide dense squish pack full      Reset to defaults Minimum copy number: Display data as a density graph: Type of graph: points bar Graph configuration help Track height: pixels (range: 11 to 128) Data view scaling: use vertical viewing range setting auto-scale to data view group auto-scale Always include zero:  OFF ON Vertical viewing range:  min:  max:   (range: 0 to 1000) Transform function: Transform data points by:  NONE LOG (ln(1+x)) Windowing function: mean+whiskers maximum mean minimum sum Smoothing window: OFF 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16  pixels Negate values: Draw y indicator lines: at y = 0.0: ON OFF    at y = OFF ON All subtracks: List subtracks: only selected/visible    all    ()   hide  Configure  AFR_BantuKenya_LP6005441-DNA_B02 wssd CN  AFR_BantuKenya_LP6005441-DNA_B02 Copy Number   Data format  hide  Configure  AFR_Ju_hoan_North_LP6005441-DNA_A11 wssd CN  AFR_Ju_hoan_North_LP6005441-DNA_A11 Copy Number   Data format  hide  Configure  AFR_Ju_hoan_North_LP6005441-DNA_B11 wssd CN  AFR_Ju_hoan_North_LP6005441-DNA_B11 Copy Number   Data format  hide  Configure  AFR_Mbuti_LP6005441-DNA_A08 wssd CN  AFR_Mbuti_LP6005441-DNA_A08 Copy Number   Data format  hide  Configure  AFR_Mbuti_LP6005441-DNA_B08 wssd CN  AFR_Mbuti_LP6005441-DNA_B08 Copy Number   Data format  hide  Configure  AMR_Piapoco_LP6005441-DNA_A04 wssd CN  AMR_Piapoco_LP6005441-DNA_A04 Copy Number   Data format  hide  Configure  AMR_Piapoco_LP6005441-DNA_B04 wssd CN  AMR_Piapoco_LP6005441-DNA_B04 Copy Number   Data format  hide  Configure  AMR_Surui_LP6005441-DNA_A12 wssd CN  AMR_Surui_LP6005441-DNA_A12 Copy Number   Data format  hide  Configure  AMR_Surui_LP6005441-DNA_B12 wssd CN  AMR_Surui_LP6005441-DNA_B12 Copy Number   Data format  hide  Configure  EAS_Han_LP6005441-DNA_C05 wssd CN  EAS_Han_LP6005441-DNA_C05 Copy Number   Data format  hide  Configure  EAS_Japanese_LP6005441-DNA_C06 wssd CN  EAS_Japanese_LP6005441-DNA_C06 Copy Number   Data format  hide  Configure  EAS_Lahu_LP6005441-DNA_B07 wssd CN  EAS_Lahu_LP6005441-DNA_B07 Copy Number   Data format  hide  Configure  EAS_Naxi_LP6005441-DNA_A09 wssd CN  EAS_Naxi_LP6005441-DNA_A09 Copy Number   Data format  hide  Configure  EAS_Naxi_LP6005441-DNA_B09 wssd CN  EAS_Naxi_LP6005441-DNA_B09 Copy Number   Data format  hide  Configure  EUR_Adygei_LP6005441-DNA_A01 wssd CN  EUR_Adygei_LP6005441-DNA_A01 Copy Number   Data format  hide  Configure  EUR_Adygei_LP6005441-DNA_B01 wssd CN  EUR_Adygei_LP6005441-DNA_B01 Copy Number   Data format  hide  Configure  EUR_Basque_LP6005441-DNA_C02 wssd CN  EUR_Basque_LP6005441-DNA_C02 Copy Number   Data format  hide  Configure  EUR_Bergamo_LP6005441-DNA_A06 wssd CN  EUR_Bergamo_LP6005441-DNA_A06 Copy Number   Data format  hide  Configure  EUR_Bergamo_LP6005441-DNA_B06 wssd CN  EUR_Bergamo_LP6005441-DNA_B06 Copy Number   Data format  hide  Configure  EUR_French_LP6005441-DNA_A05 wssd CN  EUR_French_LP6005441-DNA_A05 Copy Number   Data format  hide  Configure  EUR_French_LP6005441-DNA_B05 wssd CN  EUR_French_LP6005441-DNA_B05 Copy Number   Data format  hide  Configure  OCN_Bougainville_LP6005441-DNA_A03 wssd CN  OCN_Bougainville_LP6005441-DNA_A03 Copy Number   Data format  hide  Configure  OCN_Bougainville_LP6005441-DNA_B03 wssd CN  OCN_Bougainville_LP6005441-DNA_B03 Copy Number   Data format  hide  Configure  OCN_Papuan_LP6005441-DNA_A10 wssd CN  OCN_Papuan_LP6005441-DNA_A10 Copy Number   Data format  hide  Configure  OCN_Papuan_LP6005441-DNA_B10 wssd CN  OCN_Papuan_LP6005441-DNA_B10 Copy Number   Data format  hide  Configure  SAS_Brahui_LP6005441-DNA_C03 wssd CN  SAS_Brahui_LP6005441-DNA_C03 Copy Number   Data format  hide  Configure  SAS_Makrani_LP6005441-DNA_C07 wssd CN  SAS_Makrani_LP6005441-DNA_C07 Copy Number   Data format  hide  Configure  CHM13_kmer wssd CN  CHM13_kmer Copy Number   Data format  hide  Configure  GRCh38_kmer wssd CN  GRCh38_kmer Copy Number   Data format       Data schema/format description and download Assembly: Human Jan. 2022 (T2T CHM13v2.0/hs1) Description This track represents copy number estimates form the Simons Genome Diversity Project. 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 number Color 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 Sample Read file LP6005441-DNA_A01 /net/eichler/vol28/projects/short_read_cohorts/nobackups/SGDP/LP6005441-DNA_A01.srt.aln.bam LP6005441-DNA_A03 /net/eichler/vol28/projects/short_read_cohorts/nobackups/SGDP/LP6005441-DNA_A03.srt.aln.bam LP6005441-DNA_A04 /net/eichler/vol28/projects/short_read_cohorts/nobackups/SGDP/LP6005441-DNA_A04.srt.aln.bam LP6005441-DNA_A05 /net/eichler/vol28/projects/short_read_cohorts/nobackups/SGDP/LP6005441-DNA_A05.srt.aln.bam LP6005441-DNA_A06 /net/eichler/vol28/projects/short_read_cohorts/nobackups/SGDP/LP6005441-DNA_A06.srt.aln.bam LP6005441-DNA_A08 /net/eichler/vol28/projects/short_read_cohorts/nobackups/SGDP/LP6005441-DNA_A08.srt.aln.bam LP6005441-DNA_A09 /net/eichler/vol28/projects/short_read_cohorts/nobackups/SGDP/LP6005441-DNA_A09.srt.aln.bam LP6005441-DNA_A10 /net/eichler/vol28/projects/short_read_cohorts/nobackups/SGDP/LP6005441-DNA_A10.srt.aln.bam LP6005441-DNA_A11 /net/eichler/vol28/projects/short_read_cohorts/nobackups/SGDP/LP6005441-DNA_A11.srt.aln.bam LP6005441-DNA_A12 /net/eichler/vol28/projects/short_read_cohorts/nobackups/SGDP/LP6005441-DNA_A12.srt.aln.bam LP6005441-DNA_B01 /net/eichler/vol28/projects/short_read_cohorts/nobackups/SGDP/LP6005441-DNA_B01.srt.aln.bam LP6005441-DNA_B02 /net/eichler/vol28/projects/short_read_cohorts/nobackups/SGDP/LP6005441-DNA_B02.srt.aln.bam LP6005441-DNA_B03 /net/eichler/vol28/projects/short_read_cohorts/nobackups/SGDP/LP6005441-DNA_B03.srt.aln.bam LP6005441-DNA_B04 /net/eichler/vol28/projects/short_read_cohorts/nobackups/SGDP/LP6005441-DNA_B04.srt.aln.bam LP6005441-DNA_B05 /net/eichler/vol28/projects/short_read_cohorts/nobackups/SGDP/LP6005441-DNA_B05.srt.aln.bam LP6005441-DNA_B06 /net/eichler/vol28/projects/short_read_cohorts/nobackups/SGDP/LP6005441-DNA_B06.srt.aln.bam LP6005441-DNA_B07 /net/eichler/vol28/projects/short_read_cohorts/nobackups/SGDP/LP6005441-DNA_B07.srt.aln.bam LP6005441-DNA_B08 /net/eichler/vol28/projects/short_read_cohorts/nobackups/SGDP/LP6005441-DNA_B08.srt.aln.bam LP6005441-DNA_B09 /net/eichler/vol28/projects/short_read_cohorts/nobackups/SGDP/LP6005441-DNA_B09.srt.aln.bam LP6005441-DNA_B10 /net/eichler/vol28/projects/short_read_cohorts/nobackups/SGDP/LP6005441-DNA_B10.srt.aln.bam LP6005441-DNA_B11 /net/eichler/vol28/projects/short_read_cohorts/nobackups/SGDP/LP6005441-DNA_B11.srt.aln.bam LP6005441-DNA_B12 /net/eichler/vol28/projects/short_read_cohorts/nobackups/SGDP/LP6005441-DNA_B12.srt.aln.bam LP6005441-DNA_C02 /net/eichler/vol28/projects/short_read_cohorts/nobackups/SGDP/LP6005441-DNA_C02.srt.aln.bam LP6005441-DNA_C03 /net/eichler/vol28/projects/short_read_cohorts/nobackups/SGDP/LP6005441-DNA_C03.srt.aln.bam LP6005441-DNA_C05 /net/eichler/vol28/projects/short_read_cohorts/nobackups/SGDP/LP6005441-DNA_C05.srt.aln.bam LP6005441-DNA_C06 /net/eichler/vol28/projects/short_read_cohorts/nobackups/SGDP/LP6005441-DNA_C06.srt.aln.bam LP6005441-DNA_C07 /net/eichler/vol28/projects/short_read_cohorts/nobackups/SGDP/LP6005441-DNA_C07.srt.aln.bam LP6005441-DNA_C08 /net/eichler/vol28/projects/short_read_cohorts/nobackups/SGDP/LP6005441-DNA_C08.srt.aln.bam LP6005441-DNA_C09 /net/eichler/vol28/projects/short_read_cohorts/nobackups/SGDP/LP6005441-DNA_C09.srt.aln.bam LP6005441-DNA_C10 /net/eichler/vol28/projects/short_read_cohorts/nobackups/SGDP/LP6005441-DNA_C10.srt.aln.bam LP6005441-DNA_C11 /net/eichler/vol28/projects/short_read_cohorts/nobackups/SGDP/LP6005441-DNA_C11.srt.aln.bam LP6005441-DNA_D01 /net/eichler/vol28/projects/short_read_cohorts/nobackups/SGDP/LP6005441-DNA_D01.srt.aln.bam LP6005441-DNA_D02 /net/eichler/vol28/projects/short_read_cohorts/nobackups/SGDP/LP6005441-DNA_D02.srt.aln.bam LP6005441-DNA_D03 /net/eichler/vol28/projects/short_read_cohorts/nobackups/SGDP/LP6005441-DNA_D03.srt.aln.bam LP6005441-DNA_D04 /net/eichler/vol28/projects/short_read_cohorts/nobackups/SGDP/LP6005441-DNA_D04.srt.aln.bam LP6005441-DNA_D05 /net/eichler/vol28/projects/short_read_cohorts/nobackups/SGDP/LP6005441-DNA_D05.srt.aln.bam LP6005441-DNA_D06 /net/eichler/vol28/projects/short_read_cohorts/nobackups/SGDP/LP6005441-DNA_D06.srt.aln.bam LP6005441-DNA_D07 /net/eichler/vol28/projects/short_read_cohorts/nobackups/SGDP/LP6005441-DNA_D07.srt.aln.bam LP6005441-DNA_D08 /net/eichler/vol28/projects/short_read_cohorts/nobackups/SGDP/LP6005441-DNA_D08.srt.aln.bam LP6005441-DNA_D09 /net/eichler/vol28/projects/short_read_cohorts/nobackups/SGDP/LP6005441-DNA_D09.srt.aln.bam LP6005441-DNA_D10 /net/eichler/vol28/projects/short_read_cohorts/nobackups/SGDP/LP6005441-DNA_D10.srt.aln.bam LP6005441-DNA_D11 /net/eichler/vol28/projects/short_read_cohorts/nobackups/SGDP/LP6005441-DNA_D11.srt.aln.bam LP6005441-DNA_D12 /net/eichler/vol28/projects/short_read_cohorts/nobackups/SGDP/LP6005441-DNA_D12.srt.aln.bam LP6005441-DNA_E02 /net/eichler/vol28/projects/short_read_cohorts/nobackups/SGDP/LP6005441-DNA_E02.srt.aln.bam LP6005441-DNA_E03 /net/eichler/vol28/projects/short_read_cohorts/nobackups/SGDP/LP6005441-DNA_E03.srt.aln.bam LP6005441-DNA_E05 /net/eichler/vol28/projects/short_read_cohorts/nobackups/SGDP/LP6005441-DNA_E05.srt.aln.bam LP6005441-DNA_E06 /net/eichler/vol28/projects/short_read_cohorts/nobackups/SGDP/LP6005441-DNA_E06.srt.aln.bam LP6005441-DNA_E07 /net/eichler/vol28/projects/short_read_cohorts/nobackups/SGDP/LP6005441-DNA_E07.srt.aln.bam LP6005441-DNA_E08 /net/eichler/vol28/projects/short_read_cohorts/nobackups/SGDP/LP6005441-DNA_E08.srt.aln.bam LP6005441-DNA_E09 /net/eichler/vol28/projects/short_read_cohorts/nobackups/SGDP/LP6005441-DNA_E09.srt.aln.bam LP6005441-DNA_E10 /net/eichler/vol28/projects/short_read_cohorts/nobackups/SGDP/LP6005441-DNA_E10.srt.aln.bam LP6005441-DNA_F01 /net/eichler/vol28/projects/short_read_cohorts/nobackups/SGDP/LP6005441-DNA_F01.srt.aln.bam LP6005441-DNA_F02 /net/eichler/vol28/projects/short_read_cohorts/nobackups/SGDP/LP6005441-DNA_F02.srt.aln.bam LP6005441-DNA_F03 /net/eichler/vol28/projects/short_read_cohorts/nobackups/SGDP/LP6005441-DNA_F03.srt.aln.bam LP6005441-DNA_F04 /net/eichler/vol28/projects/short_read_cohorts/nobackups/SGDP/LP6005441-DNA_F04.srt.aln.bam LP6005441-DNA_F05 /net/eichler/vol28/projects/short_read_cohorts/nobackups/SGDP/LP6005441-DNA_F05.srt.aln.bam LP6005441-DNA_F06 /net/eichler/vol28/projects/short_read_cohorts/nobackups/SGDP/LP6005441-DNA_F06.srt.aln.bam LP6005441-DNA_F07 /net/eichler/vol28/projects/short_read_cohorts/nobackups/SGDP/LP6005441-DNA_F07.srt.aln.bam LP6005441-DNA_F08 /net/eichler/vol28/projects/short_read_cohorts/nobackups/SGDP/LP6005441-DNA_F08.srt.aln.bam LP6005441-DNA_F09 /net/eichler/vol28/projects/short_read_cohorts/nobackups/SGDP/LP6005441-DNA_F09.srt.aln.bam LP6005441-DNA_F10 /net/eichler/vol28/projects/short_read_cohorts/nobackups/SGDP/LP6005441-DNA_F10.srt.aln.bam LP6005441-DNA_F12 /net/eichler/vol28/projects/short_read_cohorts/nobackups/SGDP/LP6005441-DNA_F12.srt.aln.bam LP6005441-DNA_G02 /net/eichler/vol28/projects/short_read_cohorts/nobackups/SGDP/LP6005441-DNA_G02.srt.aln.bam LP6005441-DNA_G03 /net/eichler/vol28/projects/short_read_cohorts/nobackups/SGDP/LP6005441-DNA_G03.srt.aln.bam LP6005441-DNA_G04 /net/eichler/vol28/projects/short_read_cohorts/nobackups/SGDP/LP6005441-DNA_G04.srt.aln.bam LP6005441-DNA_G05 /net/eichler/vol28/projects/short_read_cohorts/nobackups/SGDP/LP6005441-DNA_G05.srt.aln.bam LP6005441-DNA_G06 /net/eichler/vol28/projects/short_read_cohorts/nobackups/SGDP/LP6005441-DNA_G06.srt.aln.bam LP6005441-DNA_G07 /net/eichler/vol28/projects/short_read_cohorts/nobackups/SGDP/LP6005441-DNA_G07.srt.aln.bam LP6005441-DNA_G08 /net/eichler/vol28/projects/short_read_cohorts/nobackups/SGDP/LP6005441-DNA_G08.srt.aln.bam LP6005441-DNA_G09 /net/eichler/vol28/projects/short_read_cohorts/nobackups/SGDP/LP6005441-DNA_G09.srt.aln.bam LP6005441-DNA_G10 /net/eichler/vol28/projects/short_read_cohorts/nobackups/SGDP/LP6005441-DNA_G10.srt.aln.bam LP6005441-DNA_G11 /net/eichler/vol28/projects/short_read_cohorts/nobackups/SGDP/LP6005441-DNA_G11.srt.aln.bam LP6005441-DNA_G12 /net/eichler/vol28/projects/short_read_cohorts/nobackups/SGDP/LP6005441-DNA_G12.srt.aln.bam LP6005441-DNA_H02 /net/eichler/vol28/projects/short_read_cohorts/nobackups/SGDP/LP6005441-DNA_H02.srt.aln.bam LP6005441-DNA_H03 /net/eichler/vol28/projects/short_read_cohorts/nobackups/SGDP/LP6005441-DNA_H03.srt.aln.bam LP6005441-DNA_H05 /net/eichler/vol28/projects/short_read_cohorts/nobackups/SGDP/LP6005441-DNA_H05.srt.aln.bam LP6005441-DNA_H06 /net/eichler/vol28/projects/short_read_cohorts/nobackups/SGDP/LP6005441-DNA_H06.srt.aln.bam LP6005441-DNA_H07 /net/eichler/vol28/projects/short_read_cohorts/nobackups/SGDP/LP6005441-DNA_H07.srt.aln.bam LP6005441-DNA_H08 /net/eichler/vol28/projects/short_read_cohorts/nobackups/SGDP/LP6005441-DNA_H08.srt.aln.bam LP6005441-DNA_H09 /net/eichler/vol28/projects/short_read_cohorts/nobackups/SGDP/LP6005441-DNA_H09.srt.aln.bam LP6005441-DNA_H10 /net/eichler/vol28/projects/short_read_cohorts/nobackups/SGDP/LP6005441-DNA_H10.srt.aln.bam LP6005441-DNA_H11 /net/eichler/vol28/projects/short_read_cohorts/nobackups/SGDP/LP6005441-DNA_H11.srt.aln.bam LP6005441-DNA_H12 /net/eichler/vol28/projects/short_read_cohorts/nobackups/SGDP/LP6005441-DNA_H12.srt.aln.bam LP6005442-DNA_A02 /net/eichler/vol28/projects/short_read_cohorts/nobackups/SGDP/LP6005442-DNA_A02.srt.aln.bam LP6005442-DNA_A03 /net/eichler/vol28/projects/short_read_cohorts/nobackups/SGDP/LP6005442-DNA_A03.srt.aln.bam LP6005442-DNA_A04 /net/eichler/vol28/projects/short_read_cohorts/nobackups/SGDP/LP6005442-DNA_A04.srt.aln.bam LP6005442-DNA_A08 /net/eichler/vol28/projects/short_read_cohorts/nobackups/SGDP/LP6005442-DNA_A08.srt.aln.bam LP6005442-DNA_A09 /net/eichler/vol28/projects/short_read_cohorts/nobackups/SGDP/LP6005442-DNA_A09.srt.aln.bam LP6005442-DNA_A10 /net/eichler/vol28/projects/short_read_cohorts/nobackups/SGDP/LP6005442-DNA_A10.srt.aln.bam LP6005442-DNA_A11 /net/eichler/vol28/projects/short_read_cohorts/nobackups/SGDP/LP6005442-DNA_A11.srt.aln.bam LP6005442-DNA_A12 /net/eichler/vol28/projects/short_read_cohorts/nobackups/SGDP/LP6005442-DNA_A12.srt.aln.bam LP6005442-DNA_B01 /net/eichler/vol28/projects/short_read_cohorts/nobackups/SGDP/LP6005442-DNA_B01.srt.aln.bam LP6005442-DNA_B02 /net/eichler/vol28/projects/short_read_cohorts/nobackups/SGDP/LP6005442-DNA_B02.srt.aln.bam LP6005442-DNA_B03 /net/eichler/vol28/projects/short_read_cohorts/nobackups/SGDP/LP6005442-DNA_B03.srt.aln.bam LP6005442-DNA_B04 /net/eichler/vol28/projects/short_read_cohorts/nobackups/SGDP/LP6005442-DNA_B04.srt.aln.bam LP6005442-DNA_B08 /net/eichler/vol28/projects/short_read_cohorts/nobackups/SGDP/LP6005442-DNA_B08.srt.aln.bam LP6005442-DNA_B10 /net/eichler/vol28/projects/short_read_cohorts/nobackups/SGDP/LP6005442-DNA_B10.srt.aln.bam LP6005442-DNA_B11 /net/eichler/vol28/projects/short_read_cohorts/nobackups/SGDP/LP6005442-DNA_B11.srt.aln.bam LP6005442-DNA_B12 /net/eichler/vol28/projects/short_read_cohorts/nobackups/SGDP/LP6005442-DNA_B12.srt.aln.bam LP6005442-DNA_C02 /net/eichler/vol28/projects/short_read_cohorts/nobackups/SGDP/LP6005442-DNA_C02.srt.aln.bam LP6005442-DNA_C04 /net/eichler/vol28/projects/short_read_cohorts/nobackups/SGDP/LP6005442-DNA_C04.srt.aln.bam LP6005442-DNA_C07 /net/eichler/vol28/projects/short_read_cohorts/nobackups/SGDP/LP6005442-DNA_C07.srt.aln.bam LP6005442-DNA_C10 /net/eichler/vol28/projects/short_read_cohorts/nobackups/SGDP/LP6005442-DNA_C10.srt.aln.bam LP6005442-DNA_C11 /net/eichler/vol28/projects/short_read_cohorts/nobackups/SGDP/LP6005442-DNA_C11.srt.aln.bam LP6005442-DNA_D01 /net/eichler/vol28/projects/short_read_cohorts/nobackups/SGDP/LP6005442-DNA_D01.srt.aln.bam LP6005442-DNA_D02 /net/eichler/vol28/projects/short_read_cohorts/nobackups/SGDP/LP6005442-DNA_D02.srt.aln.bam LP6005442-DNA_D03 /net/eichler/vol28/projects/short_read_cohorts/nobackups/SGDP/LP6005442-DNA_D03.srt.aln.bam LP6005442-DNA_D08 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