These statistics are generated from the BAM mapping file using the CIGAR information in tha file. The "mapped length" are the number of bases mapped to the reference. Perhaps obviously any reads that do not fully map to the reference are clipped. This clipping can either be "hard" or "soft". Within the mapping there can be "InDels" and "NotInRef"; the latter can be considered long range inserts such as could be found in reads that a split across exons for a transcriptome project.
| Mapped length | Clipping | Total reads | InDels | NotInRef | Other |
|---|---|---|---|---|---|
| 101 | Unclipped | 6,200,978 | 10,581 | 0 | 0 |
| 100 | Soft clip; Unclipped | 346,391 | 14,955 | 0 | 0 |
| 99 | Soft clip; Unclipped | 130,088 | 5,937 | 0 | 0 |
| 98 | Soft clip; Unclipped | 108,997 | 1,891 | 0 | 0 |
| 97 | Soft clip; Unclipped | 104,914 | 1,004 | 0 | 0 |
| 96 | Soft clip; Unclipped | 98,880 | 539 | 0 | 0 |
| 95 | Soft clip; Unclipped | 70,229 | 433 | 0 | 0 |
| 94 | Soft clip; Unclipped | 60,657 | 346 | 0 | 0 |
| 93 | Soft clip; Unclipped | 53,603 | 284 | 0 | 0 |
| 92 | Soft clip; Unclipped | 47,436 | 246 | 0 | 0 |
| 91 | Soft clip; Unclipped | 44,997 | 206 | 0 | 0 |
| 90 | Soft clip; Unclipped | 38,747 | 181 | 0 | 0 |
| 89 | Soft clip; Unclipped | 35,303 | 173 | 0 | 0 |
| 88 | Soft clip; Unclipped | 32,752 | 156 | 0 | 0 |
| 87 | Soft clip; Unclipped | 30,535 | 141 | 0 | 0 |
| 86 | Soft clip; Unclipped | 29,075 | 121 | 0 | 0 |
| 85 | Soft clip; Unclipped | 27,712 | 116 | 0 | 0 |
| 84 | Soft clip; Unclipped | 24,266 | 112 | 0 | 0 |
| 83 | Soft clip; Unclipped | 23,050 | 106 | 0 | 0 |
| 82 | Soft clip; Unclipped | 20,828 | 96 | 0 | 0 |
| 81 | Soft clip; Unclipped | 17,857 | 86 | 0 | 0 |
| 80 | Soft clip; Unclipped | 16,637 | 71 | 0 | 0 |
| 79 | Soft clip; Unclipped | 14,839 | 74 | 0 | 0 |
| 78 | Soft clip; Unclipped | 14,228 | 61 | 0 | 0 |
| 77 | Soft clip; Unclipped | 12,972 | 60 | 0 | 0 |
| 76 | Soft clip; Unclipped | 12,263 | 40 | 0 | 0 |
| 75 | Soft clip; Unclipped | 13,648 | 48 | 0 | 0 |
| 74 | Soft clip; Unclipped | 13,814 | 55 | 0 | 0 |
| 73 | Soft clip; Unclipped | 13,977 | 41 | 0 | 0 |
| 72 | Soft clip; Unclipped | 14,184 | 37 | 0 | 0 |
| 71 | Soft clip; Unclipped | 14,043 | 39 | 0 | 0 |
| 70 | Soft clip; Unclipped | 14,593 | 46 | 0 | 0 |
| 69 | Hard clip; Soft clip; Unclipped | 14,367 | 49 | 0 | 0 |
| 68 | Hard clip; Soft clip; Unclipped | 13,660 | 46 | 0 | 0 |
| 67 | Hard clip; Soft clip; Unclipped | 12,704 | 41 | 0 | 0 |
| 66 | Hard clip; Soft clip; Unclipped | 12,795 | 38 | 0 | 0 |
| 65 | Hard clip; Soft clip; Unclipped | 12,080 | 39 | 0 | 0 |
| 64 | Hard clip; Soft clip; Unclipped | 11,389 | 35 | 0 | 0 |
| 63 | Hard clip; Soft clip; Unclipped | 10,681 | 39 | 0 | 0 |
| 62 | Hard clip; Soft clip; Unclipped | 10,057 | 35 | 0 | 0 |
| 61 | Hard clip; Soft clip; Unclipped | 9,715 | 26 | 0 | 0 |
| 60 | Hard clip; Soft clip; Unclipped | 9,004 | 22 | 0 | 0 |
| 59 | Hard clip; Soft clip; Unclipped | 8,462 | 30 | 0 | 0 |
| 58 | Hard clip; Soft clip; Unclipped | 7,917 | 31 | 0 | 0 |
| 57 | Hard clip; Soft clip; Unclipped | 7,516 | 26 | 0 | 0 |
| 56 | Hard clip; Soft clip; Unclipped | 7,086 | 21 | 0 | 0 |
| 55 | Soft clip; Unclipped | 6,779 | 14 | 0 | 0 |
| 54 | Hard clip; Soft clip; Unclipped | 6,157 | 17 | 0 | 0 |
| 53 | Hard clip; Soft clip; Unclipped | 6,019 | 17 | 0 | 0 |
| 52 | Hard clip; Soft clip; Unclipped | 5,517 | 10 | 0 | 0 |
| 51 | Hard clip; Soft clip; Unclipped | 5,113 | 15 | 0 | 0 |
| 50 | Hard clip; Soft clip; Unclipped | 6,235 | 12 | 0 | 0 |
| 49 | Hard clip; Soft clip; Unclipped | 6,488 | 15 | 0 | 0 |
| 48 | Hard clip; Soft clip; Unclipped | 9,206 | 8 | 0 | 0 |
| 47 | Hard clip; Soft clip; Unclipped | 6,865 | 13 | 0 | 0 |
| 46 | Hard clip; Soft clip; Unclipped | 6,516 | 13 | 0 | 0 |
| 45 | Hard clip; Soft clip; Unclipped | 6,139 | 12 | 0 | 0 |
| 44 | Hard clip; Soft clip; Unclipped | 5,918 | 11 | 0 | 0 |
| 43 | Hard clip; Soft clip; Unclipped | 6,289 | 8 | 0 | 0 |
| 42 | Hard clip; Soft clip; Unclipped | 5,637 | 12 | 0 | 0 |
| 41 | Hard clip; Soft clip; Unclipped | 5,485 | 14 | 0 | 0 |
| 40 | Hard clip; Soft clip; Unclipped | 5,231 | 11 | 0 | 0 |
| 39 | Hard clip; Soft clip; Unclipped | 6,465 | 12 | 0 | 0 |
| 38 | Hard clip; Soft clip; Unclipped | 5,393 | 14 | 0 | 0 |
| 37 | Hard clip; Soft clip; Unclipped | 4,959 | 11 | 0 | 0 |
| 36 | Hard clip; Soft clip; Unclipped | 4,767 | 6 | 0 | 0 |
| 35 | Hard clip; Soft clip; Unclipped | 4,555 | 7 | 0 | 0 |
| 34 | Hard clip; Soft clip; Unclipped | 4,353 | 7 | 0 | 0 |
| 33 | Hard clip; Soft clip; Unclipped | 4,246 | 10 | 0 | 0 |
| 32 | Hard clip; Soft clip; Unclipped | 4,096 | 6 | 0 | 0 |
| 31 | Hard clip; Soft clip; Unclipped | 3,839 | 3 | 0 | 0 |
| 30 | Hard clip; Soft clip; Unclipped | 3,764 | 4 | 0 | 0 |
| 29 | Soft clip; Unclipped | 193 | 4 | 0 | 0 |
| 28 | Soft clip | 156 | 1 | 0 | 0 |
| 27 | Soft clip | 139 | 0 | 0 | 0 |
| 26 | Soft clip | 127 | 0 | 0 | 0 |
| 25 | Soft clip | 87 | 0 | 0 | 0 |
| 24 | Soft clip | 57 | 0 | 0 | 0 |
| 23 | Soft clip | 9 | 0 | 0 | 0 |
| 22 | Soft clip | 16 | 0 | 0 | 0 |
| 21 | Soft clip | 23 | 0 | 0 | 0 |
| 20 | Soft clip | 15 | 0 | 0 | 0 |
| 19 | Soft clip | 12 | 0 | 0 | 0 |
| 18 | Soft clip | 2 | 0 | 0 | 0 |
| 17 | Soft clip | 1 | 0 | 0 | 0 |
| 15 | Soft clip | 1 | 0 | 0 | 0 |
| 0 | Unclipped | 3,494 | 0 | 0 | 0 |
| TOTALS | Hard clip; Soft clip; Unclipped | 8,000,289 | 39,047 | 0 | 0 |