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Whole-genome sequencing and analysis of the Malaysian cynomolgus macaque (Macaca fascicularis) genome

Atsunori Higashino12, Ryuichi Sakate1*, Yosuke Kameoka1, Ichiro Takahashi1, Makoto Hirata1, Reiko Tanuma1, Tohru Masui1, Yasuhiro Yasutomi3 and Naoki Osada45*

Author Affiliations

1 Laboratory of Rare Disease Biospecimen, Department of Disease Bioresources Research, National Institute of Biomedical Innovation, 7-6-8 Saito-asagi, Ibaraki, Osaka 567-0085, Japan

2 Center for Human Evolution Modeling Research, Primate Research Institute, Kyoto University, Inuyama, Aichi 484-8506, Japan

3 Tsukuba Primate Research Center, National Institute of Biomedical Innovation, 1-1 Hachimandai, Tsukuba, Ibaraki 305-0843, Japan

4 Division of Evolutionary Genetics, Department of Population Genetics, National Institute of Genetics, 1111 Yata, Mishima, Shizuoka 411-8540, Japan

5 Department of Genetics, The Graduate University for Advanced Studies (SOKENDAI), 1111 Yata, Mishima, Shizuoka 411-8540, Japan

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Genome Biology 2012, 13:R58  doi:10.1186/gb-2012-13-7-r58

Published: 2 July 2012

Additional files

Additional file 1:

Figures S1 to S5 and Tables S1 to S3. Figure S1: chromosomal distribution of fold coverage of quality controlled mapped reads (duplicates and unpaired mate-pair reads were filtered out) on the reference rhesus macaque genome are shown. All chromosomes exceed 37-fold. Figure S2: minimum coverage of quality controlled mapped reads (duplicates and unpaired mate-pair reads were filtered out) on the reference rhesus macaque genome is shown. Genomic regions with at least five-fold coverage were used in the SNV analysis. Figure S3: SNV density along each chromosome. The red and blue lines represent the number of heterozygous and homozygous SNVs in 1 Mb windows, respectively. The step size of window sliding was 100 kb. Figure S4: small indel discovery rate and rhesus macaque genome quality. The red and blue lines represent the rate of small deletions and insertions, respectively, with given rhesus macaque genome sequence quality values (QVs). Small indels at sites having QV < 45 in the rhesus macaque genome sequence were filtered out. Figure S5: distribution of large-indel lengths identified in the cynomolgus macaque genome. Indels were identified using the distance information from the mate-pair libraries. Indel regions containing ambiguous genome sequences were excluded. Table S1: summary of SOLiD libraries and sequence reads (mapped to the Vietnamese cynomolgus macaque genome sequence). Table S2: pattern of nucleotide changes. Table S3: immune- and drug-response genes with completely segregating nonsynonymous SNVs between cynomolgus and rhesus macaques.

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