Puma concolor Mitochondrial DNA Consensus Sequence Files
Files from the Illumina MiSeq and HiSeq 2500 sequencing runs were processed as described (see description for Puma concolor Mitochondrial DNA Sequence Files from Illumina HiSeq 2500/MiSeq collection) and merged together using the Samtools merged command with default settings. Consensus mtDNA genome sequences for each sample were constructed using the Samtools mpileup command with the -C50 parameter to adjust the mapping quality of reads with multiple mismatches and the -q20 parameter to impose a minimum mapping quality of 20. We required minimums of 2X non-redundant sequence coverage and 80% site identity per site for consensus base calling