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Table 1 Summary of SNP detection approach

From: Development of high-throughput SNP-based genotyping in Acacia auriculiformis x A. mangium hybrids using short-read transcriptome data

SNP detection AA6 AM20 AA3 AM22
BWA     
1) Percentage of mapped reads 11.92% 11.31% 15.84% 11.57%
2) Putative SNPs 8,345 4,652 3,885 972
Bowtie     
1) Percentage of mapped reads 22.57% 21.15% 39.71% 22.21%
2) Putative SNPs 18,684 11,093 10,993 2,516
3) Number of SNPs after Filter 1 11,439 5,738 6,711 861
4) Number of SNPs after Filter 2 6,199 3,179 4,508 629
5) Number of SNPs after Filter 2 with design score >; 0.4 5,094 2,210 3,996 438
6) Validation rate of SNPs after Filter 2 50% 50% 20% 26.7%