Table 3 Accuracy of SNP predictions from ten combinations of assemblers and SNP callers with 240 authentic SNPs presented in nine carotenogenic genes in mandarin as example. The RNA-Seq was performed under the read length of 150 bp
From: A high-throughput SNP discovery strategy for RNA-seq data
No. | Paired-end read length (bp) | Assembler | SNP caller | Authentic SNPs presented | True SNPs discovered | True SNPs rate (%) | False positive SNPs predicted | False positive SNPs rate (%) |
|---|---|---|---|---|---|---|---|---|
1 | 150 | Trinity | GATK | 240 | 240 | 100.00 | 0 | 0 |
2 | 150 | Trinity | GBS | 240 | 122 | 50.83 | 0 | 0 |
3 | 150 | IDBA_tran | GATK | 240 | 32 | 13.33 | 2 | 5.88 |
4 | 150 | IDBA_tran | GBS | 240 | 25 | 10.42 | 1 | 3.85 |
5 | 150 | oases | GATK | 240 | 122 | 50.83 | 12 | 8.96 |
6 | 150 | oases | GBS | 240 | 48 | 20.00 | 6 | 11.11 |
7 | 150 | SOAPdenovo | GATK | 240 | 129 | 53.75 | 7 | 5.15 |
8 | 150 | SOAPdenovo | GBS | 240 | 88 | 36.67 | 14 | 13.73 |
9 | 150 | Trans-abyss | GATK | 240 | 193 | 80.42 | 13 | 6.31 |
10 | 150 | Trans-abyss | GBS | 240 | 94 | 39.17 | 6 | 6.00 |
Average | 150 | / | / | 240 | 109.30 | 45.54 | 6.10 | 6.10 |