Study coverage of the Arabidopsis thaliana radA mutant on cpDNA

For Illumina sequence analysis of the cpDNA, reads were aligned against the Arabidopsis reference genomes using Burrows-Wheeler Aligner (BWA) (Li et Durbin, 2009) and filtered to keep only those mapping to the cpDNA. The coverage was extracted with Bedtool genomecov (Quinlan et Hall, 2010) and coverage positions were rounded down to the upper kb and the coverage of each 1 kb-range was normalized relative to 1,000,000 total Arabidopsis reads.