Figure 4. Patterns of SV of the Ty3/gypsy retrotransposons of An. gambiae.

(A) We were able to classify 80% (462 out of 581) of the total number of proviral insertions of the Ty3/gypsy group according to their level of fragmentation (Dataset S1). The remaining 119 (20%) insertions were not classified due to unreliable alignments with respect to the respective consensus. We determined that 42% of the proviral insertions (246 out of 581) present any indel ≥10 bp: 148 (25%) are moderately-fragmented and 98 (17%) correspond to highly-fragmented insertions. On the other hand, 38% (216 out of 581) of the total number of proviral elements did not present any internal deletion or insertion ≥10 bp: 102 (18%) corresponded to true complete insertions, and the remaining 114 (20%) contain tracks of unsequenced gaps. Therefore, the total number of proviral copies with any level of fragmentation is probably underestimated. (B) We detected a total of 705 indels among the fragmented insertions of the Ty3/gypsy group of An. gambiae: 477 deletions and 228 insertions. Among deletions the most common are those with size in the range of 10–100 bp (47%), followed by those with size of 100 bp to 1 Kb (30%) and, finally, those longer than 1 Kb (23%). With respect to the insertions, the proportions were 38%, 37% and 25%, respectively.