We used BWA version 0.6.2 (Li & Durbin, 2009) to align the next generation sequencing **data** to the BTx623 sorghum reference genome sequence (version 2.1; Patterson, 2009) which was downloaded from Phytozome (Goodstein et al., 2012). Suffix array co-ordinates for each query sequence were generated using the BWA aln command with non-default parameters: "-t 8". Paired end alignments were generated using the BWA sampe command with non-default parameters: "-P -r "@RG\tID:SampleID\tSM:SampleName\tPL:Illumina" ". In the case of the single-end reads, sequence alignments were produced using the BWA samse command. Sequencing **data** and mapping statistics were obtained using the SAMtools flagstat command with default parameters. Genome coverage statistics were generated from the sequence alignment files using the combination of SAMtools and BEDTools (Quinlan & Hall, 2010). We used the SAMtools view command to uncompressed BAM files and sent the results to standard output. We then used the BEDTools genomeCoverageBed command to estimate the coverage depth from the uncompressed alignment BAM output. The SAMtools view command parameter options were "-u -q 0", while the BEDTools genomeCoverageBed command parameter options were "-ibam stdin -g ".