From: Benchmarking variant identification tools for plant diversity discovery
 | Unfiltered SNPs | Filtered SNPs | ||||||
---|---|---|---|---|---|---|---|---|
Total | Domesticated tomatoes | Wild tomatoes | Common | Total | Domesticated tomatoes | Wild tomatoes | Common | |
BWA-MEM + GATK-HC | 131,449,946 | 17,771,072 | 128,294,973 | 14,616,099 | 93,739,759 | 13,628,974 | 91,482,115 | 11,371,330 |
Bowtie2-tuned + GATK-HC | 73,393,338 | 11,813,500 | 70,453,383 | 8,873,545 | 30,307,811 | 8,261,729 | 28,243,136 | 6,197,054 |
BWA-MEM + SAMtools-mpileup | 133,734,683 | 17,268,821 | 130,886,221 | 14,420,359 | 80,709,232 | 10,366,835 | 78,727,565 | 8,385,168 |
Bowtie2-tuned + SAMtools-mpileup | 69,219,499 | 12,390,916 | 66,416,422 | 9,587,839 | 46,436,709 | 8,832,598 | 44,626,459 | 7,022,348 |