Table 2.
Comparison of PacBio and Illumina SNV calls for NA12878
| Genome | Inside GIAB | Outside GIAB | Segmental Dup. | Segmental Dup. | ||
|---|---|---|---|---|---|---|
| (1–22) | Confident | Confident | (≥95% similar) | (≥99% similar) | ||
| Region size | 2.8 Gb | 2.4 Gb | 330.7 Mb | 102.8 Mb | 47.5 Mb | |
| # SNVs | 3,518,530 | 3,002,660 | 515,870 | 180,889 | 78,851 | |
| PacBio | Ts/Tv | 2.08 | 2.14 | 1.75 | 1.95 | 1.99 |
| # SNVs | 3,563,787 | 3,065,573 | 498,214 | 116,649 | 18,684 | |
| Illumina | Ts/Tv | 2.03 | 2.1 | 1.66 | 1.84 | 1.79 |
| # SNVs | 254,428 | 63,848 | 190,580 | 103,621 | 69,705 | |
| Unique to PacBio | Ts/Tv | 1.63 | 1.83 | 1.57 | 1.9 | 1.99 |
| # SNVs | 299,733 | 126,763 | 172,970 | 39,409 | 9538 | |
| Unique to Illumina | Ts/Tv | 1.3 | 1.26 | 1.33 | 1.53 | 1.55 |
| Shared | # SNVs | 3,264,078 | 2,938,812 | 325,266 | 77,241 | 9146 |
| Illumina & PacBio | Ts/Tv | 2.12 | 2.15 | 1.85 | 2.01 | 2.04 |
Variants were called using short reads (33× coverage) with FreeBayes and using SMS long reads (30× coverage) with Longshot. The number of variants called by each technology, the number of variants shared between the two technologies, and the corresponding transition/transversion (Ts/Tv) ratios are shown for the whole genome and various subsets of the genome including GIAB high-confidence regions and segmental duplications with high sequence identity