Table 3.
Statistical Significance of the Association of Short Direct Repeats (DRs) With Deletions
|
|
|
|
|
No. of repeats in randomization test (Test 1) |
|
|
No. of matching bases in randomization test (Test 2) |
||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| LTR Retrotransposon Family |
No. of elements |
No. of deletions |
No. of deletions flanked by DRsa |
Mean ± SD (max.) |
P |
No. of bases in repeats |
No. of bases matching in 5′ and 3′ sequences |
Mean ± SD (max.) |
P |
||
| Family I (Osr4) | 20 | 15 | 14 | 0.44 ± 0.64 (4) | 6 × 10-10 | 54 | 51 | 14.9 ± 3.2 (26) | 4 × 10-9 | ||
| Family X (Osr1) | 20 | 9 | 8 | 0.35 ± 0.56 (3) | 1 × 10-7 | 38 | 38 | 10.2 ± 2.28 (19) | 7 × 10-7 | ||
| Family XI (Osr41) | 20 | 47 | 41 | 1.23 ± 1.09 (6) | 8 × 10-10 | 207 | 193 | 52.7 ± 6.2 (74) | 9 × 10-29 | ||
| Osr8 | 10 | 16 | 13 | 0.26 ± 0.47 (2) | 2 × 10-14 | 63 | 63 | 15.0 ± 4.0 (29) | 7 × 10-8 | ||
| Osr30
|
10
|
12
|
10
|
0.28 ± 0.50 (3)
|
7 × 10-11
|
44
|
43
|
11.3 ± 3.7 (23)
|
5 × 10-5
|
||
-
↵a A short direct repeat (DR) was considered as starting from the deletion breakpoint and was extended if the bases in the 5′ and 3′ flanking sequences matched, or if a single-base mismatch was followed by at least two matching bases. The DR was considered as stopping where a mismatch was followed by zero or one matching base
