################################################################### #1001 Genomes Salk Contribution Data Description ################################################################### Data analysis description: The genomes have been analyzed separately and in a joint approach. First, each of the genomes was analyzed separately using the short read pipeline SHORE (Ossowski et al, Genome Res, 2008). The specific aligner we used was BWA (Li H. and Durbin R., Bioinformatics, 2009). Within these folder are 3 files which are described in the following: |-- |--quality_variant_filtered_.txt |--quality_variant_.txt |--unsequenced_.txt ################################################################### # Strain folders: File content description. ################################################################### Each of the following files is in a tab-delimited format. quality_variant_.txt This file contains all potential SNPs and 1-bp deletions regardless of the quality of the call. Column Format: <# of nonrepetitive reads supporting substituion> quality_variant_filtered_.txt This file contains a list of SNPs and 1-bp deletions with a quality score of 25 and above. Column Format: <# of nonrepetitive reads supporting substituion> unsequenced_.txt This file contains a list of ranges that did not have sequence coverage. Column Format: <#N> <# repetitive positions>