Table 3 Sample and reference genome comparison statistics

C1

43780932

41030531 (93.72%)

26896549 (61.43%)

14133982 (32.28%)

13468455 (30.76%)

13428094 (30.67%)

13431244 (30.68%)

13465305 (30.76%)

97.84%

1.45%

C2

39434346

37476740 (95.04%)

23075521 (58.52%)

14401219 (36.52%)

11561094 (29.32%)

11514427 (29.2%)

11515459 (29.2%)

11560062 (29.31%)

98.03%

1.32%

C3

45533344

43811184 (96.22%)

24330750 (53.44%)

19480434 (42.78%)

12198066 (26.79%)

12132684 (26.65%)

12133320 (26.65%)

12197430 (26.79%)

99.04%

0.64%

C4

41601340

39450866 (94.83%)

28569365 (68.67%)

10881501 (26.16%)

14299447 (34.37%)

14269918 (34.3%)

14245105 (34.24%)

14324260 (34.43%)

98.05%

1.36%

C5

44047466

42090565 (95.56%)

28808366 (65.4%)

13282199 (30.15%)

14470240 (32.85%)

14338126 (32.55%)

14356012 (32.59%)

14452354 (32.81%)

98.39%

1.11%

S1

42447828

39535118 (93.14%)

34962023 (82.36%)

4573095 (10.77%)

17420811 (41.04%)

17541212 (41.32%)

17467140 (41.15%)

17494883 (41.22%)

94.54%

4.17%

S2

38825744

36475226 (93.95%)

35255785 (90.81%)

1219441 (3.14%)

17549530 (45.2%)

17706255 (45.6%)

17608073 (45.35%)

17647712 (45.45%)

86.12%

11.79%

S3

46735142

43343607 (92.74%)

39928429 (85.44%)

3415178 (7.31%)

19897050 (42.57%)

20031379 (42.86%)

19953319 (42.69%)

19975110 (42.74%)

96.32%

2.77%

S4

23893386

21367004 (89.43%)

21173685 (88.62%)

193319 (0.81%)

10572481 (44.25%)

10601204 (44.37%)

10534396 (44.09%)

10639289 (44.53%)

91.73%

4.26%

E1

37064522

31743451 (85.64%)

29091267 (78.49%)

2652184 (7.16%)

14557649 (39.28%)

14533618 (39.21%)

14526902 (39.19%)

14564365 (39.29%)

91.35%

5.85%

E2

29075142

27609750 (94.96%)

27381280 (94.17%)

228470 (0.79%)

13707519 (47.15%)

13673761 (47.03%)

13651029 (46.95%)

13730251 (47.22%)

98.80%

0.44%

E3

31400410

28185248 (89.76%)

27716167 (88.27%)

469081 (1.49%)

13816279 (44.0%)

13899888 (44.27%)

13840701 (44.08%)

13875466 (44.19%)

98.44%

0.64%