Table 4 Summary of SNP discovery results for F. grandifolia using the reference transcriptomes generated by DNASTAR NGEN and Newbler
Statistics | DNASTAR Reference Transcriptome | Newbler Reference Transcriptome |
|---|---|---|
Number of Contigs in Reference | 43,212 | 14,977 |
Number of Bases in Reference | 28,676,242 | 11,580,835 |
Number of Mapped Reads (%) | 1,357,629 (96.55%) | 938,418 (88.82%) |
Number of Mapped Bases (%) | 494,805,288 (97.45%) | 312,081,222 (85.48%) |
Fully Mapped Reads (%) | 444,838 (31.64%) | 396,609 (37.54%) |
Partially Mapped Reads (%) | 35,728 (2.54%) | 135,858 (12.86%) |
Non-Unique Mapped Reads (%) | 871,685 (61.99%) | 147,210 (13.93%) |
Chimeric Reads (%) | 5378 (0.38%) | 258,741 (24.49%) |
Unmapped Reads (%) | 32,025 (2.28%) | 101,623 (9.62%) |
Reads Too Short (%) | 16,470 (1.17%) | 16,470 (1.56%) |
High Confidence SNP Calls | 2119 (12,069) | 15,542 (14,574) |
HC SNP Calls (Not Ambiguous) | 10,971 (10,934) | 15,541 (14,573) |