Table 2.
Statistical Significance of the Association of Short Repeats with Deletions and Tandem Duplications
| LTR retrotransposon family | Elements | Deletions/duplications | No. flanked by short DRsa | No. of repeats in randomization test (Test 1) | Bases in repeats | Bases matching in 5′ and 3′ sequences | No. of matching bases in randomization test (Test 2) | ||
|---|---|---|---|---|---|---|---|---|---|
| Mean ± SD (max.) | P | Mean ± SD (max.) | P | ||||||
| (a) Deletions | |||||||||
| Family 1 | 5 | 6 | 6 | 0.18 ± 0.43 (3) | 3 × 10−11 | 40 | 37 | 9.5 ± 2.5 (19) | 2 × 10−7 |
| Family 2 | 5 | 8 | 4 | 0.17 ± 0.38 (2) | 6 × 10−9 | 18 | 18 | 4.8 ± 1.8 (10) | 4 × 10−4 |
| Family 3 | 33 | 59 | 46 | 0.64 ± 0.79 (4) | 6 × 10−15 | 281 | 251 | 62.6 ± 6.9 (87) | 4 × 10−34 |
| All three families | 43 | 73 | 56 | 0.85 ± 0.90 (5) | 3 × 10−14 | 339 | 306 | 76.6 ± 7.4 (101) | 2 × 10−41 |
| (b) Tandem duplications | |||||||||
| Family 3 | 6 | 6 | 6 | 0.20 ± 0.44 (2) | 2 × 10−10 | 26 | 25 | 6.2 ± 2.2 (15) | 8 × 10−5 |
a
A repeat was considered as starting from the deletion or duplication breakpoint and was extended if the bases in the 5′ and 3′ flanking sequences matched or (if there was a mismatching base) that mismatch was followed by at least 2 matching bases. The repeat was considered as stopping where a mismatch was followed by only 1 matching base.