Table 1 RNA-Seq analysis statistics.

From: Transcriptional response to the host cell environment of a multidrug-resistant Mycobacterium tuberculosis clonal outbreak Beijing strain reveals its pathogenic features

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%)

  1. aThe percentages are with respect to the total read numbers.
  2. bWith respect to the high-quality reads.
  3. cWith respect to the “non-human” reads.
  4. dWith respect to the total aligned reads.
Back to article page