Table 1.
RNA-Seq analysis statistics.
| Experiment | Rep | Total reads | High-quality readsa | “Non-human” readsb | Aligned reads | Unaligned readsc | |||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| Genesd | Ambiguousd | Low alignment qualityd | No featured | Total aligned readsc | |||||||
| H35Rv | Log phase | 1 | 40,436,194 | 37,494,942 (92.72%) | N/A | 35,595,491 (95.46%) | 479,559 (1.29%) | 1,077,625 (2.89%) | 137,077 (0.37%) | 37,289,752 (99.45%) | 205,190 (00.55%) |
| 2 | 33,260,151 | 29,975,555 (90.12%) | N/A | 28,417,810 (95.25%) | 424,760 (1.42%) | 881,165 (2.95%) | 110,753 (0.37%) | 29,834,488 (99.53%) | 141,067 (00.47%) | ||
| 3 | 43,495,077 | 41,052,086 (94.38%) | N/A | 38,715,994 (94.90%) | 563,711 (1.38%) | 1,391,300 (3.41%) | 125,766 (0.31%) | 40,796,771 (99.38%) | 255,315 (00.62%) | ||
| T = 0 | 1 | 69,384,126 | 39,788,385 (57.34%) | 10,272,043 (25.81%) | 5,668,715 (93.14%) | 30,144 (0.50%) | 360,156 (5.92%) | 27,449 (0.45%) | 6,086,464 (59.25%) | 4,185,579 (40.75%) | |
| 2 | 49,069,412 | 43,216,311 (88.54%) | 11,533,518 (26.69%) | 5,721,097 (91.23%) | 33,815 (0.54%) | 487,648 (7.78%) | 28,216 (0.45%) | 6,270,776 (54.37%) | 5,262,742 (45.63%) | ||
| 3 | 61,793,448 | 44,645,773 (72.25%) | 11,871,446 (26.59%) | 7,903,746 (94.92%) | 61,297 (0.74%) | 324,871 (3.90%) | 36,578 (0.44%) | 8,326,492 (70.14%) | 3,544,954 (29.86%) | ||
| T = 4 | 1 | 51,499,003 | 45,381,707 (88.12%) | 11,771,501 (27.44%) | 6,795,028 (94.13%) | 31,231 (0.43%) | 356,495 (4.94%) | 35,934 (0.50%) | 7,218,688 (61.32%) | 4,552,813 (38.68%) | |
| 2 | 37,533,515 | 31,889,646 (84.96%) | 9,166,172 (28.74%) | 5,502,028 (94.17%) | 27,182 (0.47%) | 282,361 (4.83%) | 31,280 (0.54%) | 5,842,851 (63.74%) | 3,323,321 (36.26%) | ||
| 3 | 49,834,123 | 35,893,654 (72.03%) | 12,408,152 (34.56%) | 7,383,233 (92.19%) | 33,263 (0.42%) | 551,458 (6.89%) | 40,899 (0.51%) | 8,008,853 (64.55%) | 4,399,299 (35.45%) | ||
| MKR | Log phase | 1 | 47,208,119 | 41,914,952 (88.79%) | N/A | 39,736,298 (95.23%) | 610,170 (1.46%) | 1,194,226 (2.86%) | 187,760 (0.45%) | 41,728,454 (99.56%) | 186,498 (00.44%) |
| 2 | 35,798,457 | 28,025,257 (78.28%) | N/A | 26,981,068 (96.68%) | 315,930 (1.13%) | 495,136 (1.77%) | 115,074 (0.41%) | 27,907,208 (99.58%) | 118,049 (00.42%) | ||
| 3 | 39,691,565 | 33,012,205 (83.17%) | N/A | 31,828,612 (96.83%) | 530,170 (1.61%) | 401,351 (1.22%) | 110,259 (0.34%) | 32,870,392 (99.57%) | 141,813 (00.43%) | ||
| T = 0 | 1 | 59,984,975 | 47,217,791 (78.72%) | 8,170,834 (17.31%) | 3,099,773 (93.47%) | 12,993 (0.39%) | 185,047 (5.58%) | 18,406 (0.56%) | 3,316,219 (40.59%) | 4,854,615 (59.41%) | |
| 2 | 51,631,051 | 47,992,656 (92.95%) | 6,447,278 (13.43%) | 1,688,256 (93.86%) | 7,241 (0.40%) | 93,583 (5.20%) | 9,526 (0.53%) | 1,798,606 (27.90%) | 4,648,672 (72.10%) | ||
| 3 | 49,822,302 | 45,605,000 (91.53%) | 7,876,348 (17.27%) | 2,845,379 (93.46%) | 13,139 (0.43%) | 170,620 (5.60%) | 15,255 (0.50%) | 3,044,393 (38.65%) | 4,831,955 (61.35%) | ||
| T = 4 | 1 | 53,928,086 | 46,705,940 (86.61%) | 6,740,593 (14.43%) | 1,993,218 (94.22%) | 6,129 (0.29%) | 103,377 (4.89%) | 12,736 (0.60%) | 2,115,460 (31.38%) | 4,625,133 (68.62%) | |
| 2 | 33,601,205 | 29,535,628 (87.90%) | 5,426,088 (18.37%) | 1,155,969 (91.32%) | 3,664 (0.29%) | 99,314 (7.85%) | 6,863 (0.54%) | 1,265,810 (23.33%) | 4,160,278 (76.67%) | ||
| 3 | 38,471,145 | 27,503,371 (71.50%) | 5,483,082 (19.94%) | 1,618,957 (92.98%) | 4,674 (0.27%) | 107,999 (6.20%) | 9,525 (0.55%) | 1,741,155 (31.76%) | 3,741,927 (68.24%) | ||
aThe percentages are with respect to the total read numbers.
bWith respect to the high-quality reads.
cWith respect to the “non-human” reads.
dWith respect to the total aligned reads.