File_S2_FILLINFindHaplotypes_output.zip (161.39 MB)
File_S2_FILLINFindHaplotypes_output.zip
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dataset
modified on 2019-03-23, 15:38 Brief description
This zip file contains output from the FILLINFindHaplotypes Plugin available in TASSEL 5 (https://www.maizegenetics.net/tassel). Input SNP data were 11.3 million SNPs on 212 samples all from the public Maize HapMap 3.2.1 (Bukowski et al. 2018). The plugin was run with the following settings: window size of 2,000 SNPs, maximum diversity 3%,
maximum heterozygosity 5%, maximum missing in a sample within a haplotype
block 40%, and minimum number of samples required to form a haplotype group 1.
File explanations
There are 2 files for each haplotype block (window of 2000 SNPs). Each filename contains the chromosome number and the haplotype block number. Filenames ending in .haplotypes.txt contain the haplotype group names and all of the samples that were placed into each haplotype group. Filenames ending in .hmp.txt contain the individual consensus SNP calls observed by haplotype group for that SNP window.
Examples
mintaxa1_mxdiv03_mxhet05_c6.gc6s445.hmp.txt - contains the consensus SNP calls for each haplotype group for chromosome 6 haplotype block 445
mintaxa1_mxdiv03_mxhet05_c6s445.haplotypes.txt - contains the haplotype groups and corresponding samples for chromosome 6 haplotype block 445. For example, the 2nd haplotype group within this file is named h10282set_B164:d3. This haplotype group contains the samples 282set_B164, RS710, and 282set_R4.
