Cheetah Tool 2019 V1.0

The three mitogenomes were reconstructed using next generation sequence (IonTorrent PGM), followed by validation of SNPs by various methods (see above). After exploring data quality using FastQC v0.11.520, we used a custom script to drop unterminated reads and remove adaptors and primers. We then used Trimmomatic v0.3421 to trim low-quality reads (LEADING:20 TRAILING:20 SLIDINGWINDOW:4:15 MINLEN:18). We then aligned reads to the A. j. jubatus mtDNA reference sequence (NC_005212) using Bowtie 2.022 and end-to-end alignment and the -very-sensitive flag. After converting to.bam format using samtools23 we proceeded with SNP calling using GATK v3.7-0gcfedb6724. We applied base recalibration using a manually generated set of reference SNPs based on published cheetah mtDNA (for a list of samples used see Table S1) before SNP calling using default parameter settings. We hard filtered SNP calls (DP 10.0 MQ

Cheetah Tool 2019 V1.0

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