Table 1 Classification of indels from 115 re-sequenced cucumber samples
InDel Class | Number | Rate |
|---|---|---|
Single bases | 4,481,885 | 57.15% |
A | 1,749,883 | 22.31% |
T | 1,742,058 | 22.21% |
C | 496,833 | 6.33% |
G | 493,111 | 6.29% |
Repeat Expansions | 3,118,580 | 39.76% |
Monomeric (4/4) | 703,289 | 8.97% |
(T)n | 332,623 | 4.24% |
(A)n | 331,437 | 4.23% |
(C)n | 19,834 | 0.25% |
(G)n | 19,395 | 0.25% |
Dimeric (12/12) | 1,139,311 | 14.53% |
(AT)n | 244,447 | 3.12% |
(TA)n | 224,719 | 2.87% |
(AG)n | 107,640 | 1.37% |
(TC)n | 102,126 | 1.30% |
(TG)n | 94,232 | 1.20% |
(AC)n | 89,467 | 1.14% |
Other (NN)n | 276,680 | 3.53% |
Trimeric (60/60) | 678,902 | 8.66% |
(AAG)n | 678,902 | 8.66% |
(AAT)n | 40,479 | 0.52% |
(TTC)n | 35,863 | 0.46% |
(CTT)n | 31,313 | 0.40% |
(ATT)n | 31,432 | 0.40% |
(AAC)n | 25,933 | 0.33% |
Other (NNN)n | 513,882 | 6.53% |
Tetrameric (245/252) | 144,843 | 1.85% |
Pentameric (1009/1020) | 157,633 | 2.01% |
Hexameric (3613/4092) | 36,854 | 0.47% |
Heptameric (6813/16380) | 103,379 | 1.32% |
Octameric (9002/65532) | 69,310 | 0.88% |
Nomameric (9772/262140) | 26,537 | 0.34% |
Decameric (9927/1048572) | 58,522 | 0.75% |
Transposons | 269 | 0.00% |
other | 242,212 | 3.09% |
total | 7,842,946 | Â |