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Cheetah Tool 2019 V1.0 ~UPD~

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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