|
Types of error |
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| Error type |
Number of occurrences |
Percent of errors |
Error rate |
|
|
|||
| Insertions |
58,337 |
36% |
0.18% |
| Homopolymer extension and CAFIE |
32,858 |
20% |
0.10% |
| Not associated with homopolymers |
25,479 |
16% |
0.08% |
| Deletions |
43,107 |
27% |
0.13% |
| Incomplete homopolymer extension |
13,868 |
9% |
0.04% |
| Not associated with homopolymers |
29,239 |
18% |
0.09% |
| Mismatches |
25,281 |
16% |
0.08% |
| Homopolymer extension and CAFIE |
16,725 |
10% |
0.05% |
| Not associated with homopolymers |
8,556 |
5% |
0.03% |
| Ambiguous base calls (N) |
34,184 |
21% |
0.10% |
|
|
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| Read errors |
Number of occurrences |
Cumulative percent of reads |
Percent of reads |
|
|
|||
| Reads with no errors (perfect match) |
279,468 |
82% |
82% |
| Reads with no more than one error |
35,813 |
93% |
11% |
| Reads with no more than two errors |
11,651 |
96% |
3% |
| Reads with more than two errors |
13,218 |
100% |
4% |
|
Errors were classified as insertions, deletions, mismatches (substitutions) and ambiguous base calls (Ns). We further classified insertions, deletions and mismatches by their association with homopolymer effects. Deletions corresponding to an adjacent base are considered incomplete extension. Insertions and mismatches of the same base as an adjacent base are extensions. Insertions and mismatches that are the same as an upcoming homopolymer with no more than two intervening bases are considered carry forward errors. | |||
Huse et al. Genome Biology 2007 8:R143 doi:10.1186/gb-2007-8-7-r143 |
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