Table 2 Accuracy of SNP predictions from ten combinations of assemblers and SNP callers with 40 authentic SNPs presented in five anthocyanin biosynthesis related genes in peach as example. The RNA-Seq was performed under the read lengths of 125 bp and 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 | 125 | Trinity | GATK | 40 | 25 | 62.50 | 11 | 30.56 |
2 | 125 | Trinity | GBS | 40 | 14 | 35.00 | 10 | 41.67 |
3 | 125 | IDBA_tran | GATK | 40 | 28 | 70.00 | 16 | 36.36 |
4 | 125 | IDBA_tran | GBS | 40 | 0 | 0 | 0 | 0 |
5 | 125 | oases | GATK | 40 | 32 | 80.00 | 40 | 55.56 |
6 | 125 | oases | GBS | 40 | 3 | 7.50 | 9 | 75.00 |
7 | 125 | SOAPdenovo | GATK | 40 | 23 | 57.50 | 5 | 17.86 |
8 | 125 | SOAPdenovo | GBS | 40 | 5 | 12.50 | 3 | 37.50 |
9 | 125 | Trans-abyss | GATK | 40 | 24 | 60.00 | 8 | 25.00 |
10 | 125 | Trans-abyss | GBS | 40 | 3 | 7.50 | 1 | 25.00 |
Average | 125 | / | / | 40 | 15.70 | 39.25 | 10.30 | 34.45 |
11 | 150 | Trinity | GATK | 40 | 40 | 100.00 | 0 | 0 |
12 | 150 | Trinity | GBS | 40 | 6 | 15.00 | 0 | 0 |
13 | 150 | IDBA_tran | GATK | 40 | 28 | 70.00 | 4 | 12.50 |
14 | 150 | IDBA_tran | GBS | 40 | 6 | 15.00 | 2 | 25.00 |
15 | 150 | oases | GATK | 40 | 39 | 97.50 | 1 | 2.50 |
16 | 150 | oases | GBS | 40 | 6 | 15.00 | 0 | 0 |
17 | 150 | SOAPdenovo | GATK | 40 | 35 | 87.50 | 3 | 7.89 |
18 | 150 | SOAPdenovo | GBS | 40 | 6 | 15.00 | 0 | 0 |
19 | 150 | Trans-abyss | GATK | 40 | 33 | 82.50 | 5 | 13.16 |
20 | 150 | Trans-abyss | GBS | 40 | 2 | 5.00 | 0 | 0 |
Average | 150 | / | / | 40 | 20.10 | 50.25 | 1.50 | 6.11 |