Table 3.
Exons with frequent low coverage.a
| Gene (exon) | SureSelect | TargetSeq | TruSeq | GC content (%) | Other observations |
|---|---|---|---|---|---|
| APOB (1) | 12 | 33 | 12 | 79 | |
| BRCA1 (1) | 12 | 33 | 0 | 56 | Pseudogene |
| BRCA2 (18) | 0 | 0 | 8 | 41 | |
| CACNA1S (18) | 0 | 0 | 12 | 56 | |
| DSG2 (1) | 0 | 6 | 12 | 73 | Pseudogene |
| KCNH2 (1) | 4 | 30 | 8 | 65 | |
| KCNH2 (2) | 7 | 27 | 2 | 75 | |
| KCNH2 (4) | 5 | 32 | 0 | 69 | |
| KCNH2 (12) | 6 | 0 | 0 | 66 | |
| KCNH2 (13) | 12 | 33 | 12 | 78 | |
| KCNQ1 (1) | 12 | 33 | 12 | 77 | |
| LDLR (1) | 5 | 33 | 12 | 67 | |
| MEN1 (10) | 2 | 24 | 0 | 66 | |
| MSH6 (1) | 11 | 31 | 0 | 72 | |
| MYH7 (27) | 11 | 2 | 0 | 65 | |
| PCSK9 (9) | 6 | 0 | 0 | 65 | |
| PKP2 (1) | 2 | 23 | 12 | 71 | |
| PKP2 (6) | 6 | 20 | 0 | 58 | |
| PMS2 (2) | 12 | 7 | 0 | 46 | |
| PMS2 (3) | 12 | 6 | 0 | 38 | |
| PMS2 (4) | 5 | 32 | 0 | 46 | |
| PMS2 (5) | 12 | 6 | 0 | 49 | |
| PMS2 (12) | 12 | 6 | 0 | 45 | Pseudogene |
| PMS2 (14) | 11 | 6 | 0 | 55 | Pseudogene |
| PMS2 (15) | 10 | 0 | 0 | 52 | Pseudogene |
| PRKAG2 (5) | 0 | 18 | 4 | 72 | |
| RB1 (1) | 12 | 33 | 4 | 76 | Pseudogene |
| RET (1) | 1 | 27 | 0 | 68 | Pseudogene |
| RYR1 (28) | 0 | 16 | 0 | 70 | Pseudogene |
| RYR1 (33) | 7 | 5 | 0 | 67 | Pseudogene |
| RYR1 (35) | 4 | 0 | 12 | 50 | Pseudogene |
| RYR1 (75) | 0 | 0 | 11 | 60 | Pseudogene |
| RYR1 (90) | 12 | 33 | 12 | 76 | Pseudogene |
| RYR2 (1) | 5 | 32 | 12 | 48 | Pseudogene |
| RYR2 (5) | 5 | 25 | 11 | 20 | Pseudogene, Repetitive DNA |
| RYR2 (6) | 0 | 26 | 12 | 36 | Pseudogene |
| RYR2 (82) | 0 | 22 | 10 | 57 | Pseudogene |
| RYR2 (93) | 0 | 0 | 11 | 36 | Pseudogene |
| SCN5A (1) | 12 | 33 | 12 | 81 | |
| SCN5A (28) | 7 | 27 | 0 | 56 | |
| SDHC (2) | 0 | 0 | 12 | 54 | Pseudogene |
| SDHC (4) | 0 | 0 | 11 | 56 | Pseudogene |
| SDHC (5) | 6 | 6 | 12 | 46 | Pseudogene |
| SDHD (4) | 12 | 6 | 0 | 49 | |
| TGFBR1 (1) | 12 | 33 | 12 | 84 | Pseudogene |
| TSC2 (34) | 0 | 23 | 0 | 67 | Pseudogene |
| VHL (1) | 6 | 14 | 0 | 72 | Pseudogene |
| WT1 (1) | 7 | 28 | 6 | 73 |
a
Listed are the genes and corresponding exons which had low coverage (<100% of nucleotides at ≥20× depth) in more than half the samples examined. For both the gene symbols and names of the genes used in this table, see the human genes footnote in this article.