Single Nucleotide Polymorphisms for Monodelphis domestica

SNPs were discovered in the Monodelphis domestica genome sequence (monDom4 - Jan 2006) as a standard part of the genome assembly process. Such SNPs represent cases where the sequenced individual I1438 (SFBR Population 1) was heterozygous. Assembly SNPs were only called within certified sequences, and if each allele was observed at least twice, implying that ≥4 separate shotgun reads aligned to the base containing the putative SNP.

Additional SNPs were discovered by low-coverage shotgun sequencing of three stocks frequently used in laboratory research: B5539 (SFBR Population 1; 104,042 passing reads), D3508 (SFBR Population 2; 100,000 reads), and C5181 (SFBR Population 5; 99,212 reads). Reads were placed on the MonDom4 assembly and SNPs were discovered using SSAHA-SNP.

The files provided include 1,284,726 SNPs in total distributed across chromosomes 1-8 and X. Numbers in the file names denote position on this assembly.

http://www.broad.mit.edu/pub/monodelphis_snp_release/

File Name SNPs Included
Chr1_239802096_to_297136579_SNPs.xls 60000
Chr1_297136579_to_546660765_SNPs.xls 60000
Chr1_546660765_to_582233046_SNPs.xls 60000
Chr1_582233046_to_713128631_SNPs.xls 60000
Chr1_713128631_to_748016583_SNPs.xls 7144
Chr1_849_to_239802096_SNPs.xls 60000
Chr2_180307803_to_416913171_SNPs.xls 60000
Chr2_416913171_to_541553955_SNPs.xls 24084
Chr2_96844_to_180307803_SNPs.xls 60000
Chr3_105515553_to_141110080_SNPs.xls 60000
Chr3_141110080_to_194966732_SNPs.xls 60000
Chr3_194966732_to_436047529_SNPs.xls 60000
Chr3_436047529_to_526104421_SNPs.xls 29468
Chr3_474_to_105515553_SNPs.xls 60000
Chr4_1940_to_229775036_SNPs.xls 60000
Chr4_229775036_to_274286626_SNPs.xls 60000
Chr4_274286626_to_371061142_SNPs.xls 60000
Chr4_371061142_to_430122506_SNPs.xls 57083
Chr5_1154_to_308702178_SNPs.xls 59037
Chr6_2475_to_244781654_SNPs.xls 50873
Chr7_205060586_to_262623480_SNPs.xls 14934
Chr7_4528_to_205060586_SNPs.xls 60000
Chr8_103076399_to_276633053_SNPs.xls 60000
Chr8_276633053_to_308442250_SNPs.xls 5947
Chr8_3024347_to_103076399_SNPs.xls 60000
ChrX_3000707_to_60618598_SNPs.xls 16156