Analysis of the second batch of NimbleGen capture data
/home/kunzhang/CpgMIP/MONOD/Data/141112_HiSeqRapidRun/get_capture_stats.pl /media/Ext12T/DD_Ext12T/MONOD/141216_HiSeqRapidRun/BAMfiles > 141216_HiSeqRapidRun.capture_stats.txt
Sample
|
total_bases_coverred
|
total_bases
|
on_target_bases_covered
|
on_target_bases
|
Specificity
|
Enrichment_factor
|
6-P-1 |
496,391,712 |
883,938,352 |
20,732,014 |
236,943,256 |
26.81% |
37
|
6-P-2 |
598,767,372 |
974,626,668 |
31,706,660 |
246,684,036 |
25.31% |
34
|
6-P-3 |
543,413,415 |
1,131,193,408 |
31,995,541 |
417,353,349 |
36.89% |
59
|
6T-1 |
729,794,959 |
1,070,341,509 |
30,151,406 |
155,220,183 |
14.50% |
17
|
6T-2 |
784,299,649 |
1,158,440,912 |
29,456,650 |
159,710,882 |
13.79% |
16
|
6T-3 |
1,452,467,042 |
3,323,804,083 |
33,406,665 |
627,923,179 |
18.89% |
24
|
6T-4 |
764,174,440 |
1,132,324,550 |
30,925,708 |
176,622,088 |
15.60% |
19
|
6T-5 |
843,555,327 |
1,282,158,923 |
30,892,326 |
198,472,950 |
15.48% |
19
|
7-P-10 |
465,462,705 |
897,601,881 |
10,665,677 |
208,435,905 |
23.22% |
31
|
7-P-3 |
376,857,145 |
703,513,104 |
10,510,561 |
173,576,316 |
24.67% |
33
|
7-P-5 |
536,571,852 |
807,646,898 |
30,738,662 |
181,239,774 |
22.44% |
29
|
7-P-6 |
616,774,497 |
1,108,444,523 |
20,513,185 |
265,799,682 |
23.98% |
32
|
7-P-7 |
658,461,220 |
1,111,809,575 |
20,479,249 |
228,609,307 |
20.56% |
26
|
7-P-8 |
439,982,190 |
839,669,742 |
11,446,574 |
201,598,027 |
24.01% |
32
|
7T-1 |
780,242,147 |
1,137,145,477 |
30,063,836 |
160,294,067 |
14.10% |
17
|
7T-2 |
746,306,547 |
1,175,101,409 |
26,503,015 |
173,809,990 |
14.79% |
18
|
7T-4 |
771,225,069 |
1,142,595,127 |
29,851,920 |
171,599,332 |
15.02% |
18
|
7T-5 |
802,376,647 |
1,227,075,648 |
27,971,718 |
179,541,336 |
14.63% |
17
|
NC-7 |
255,231,717 |
1,119,499,850 |
7,739,071 |
425,057,131 |
37.97% |
62
|
PC-P_2 |
563,439,590 |
865,434,623 |
30,337,168 |
193,164,906 |
22.32% |
29
|
PC-P_4 |
527,669,028 |
840,929,316 |
29,831,801 |
207,852,537 |
24.72% |
33
|
PC-P_9 |
559,749,434 |
1,035,542,788 |
24,069,681 |
289,633,563 |
27.97% |
39
|
PCT-1 |
714,410,318 |
1,064,633,702 |
27,058,939 |
155,196,610 |
14.58% |
17
|
PCT-2 |
726,354,565 |
1,275,756,897 |
19,580,892 |
189,203,593 |
14.83% |
18
|
PCT-4 |
815,323,371 |
1,247,319,961 |
28,462,046 |
179,280,115 |
14.37% |
17
|
PCT-6 |
948,428,968 |
1,450,561,748 |
31,894,490 |
214,220,998 |
14.77% |
18
|
PCT-7 |
796,647,247 |
1,191,900,342 |
31,314,595 |
191,113,213 |
16.03% |
19
|
|
- Here is the results for the first capture experiment (141112_SN1001).
Sample
|
total_bases_coverred
|
total_bases
|
on_target_bases_covered
|
on_target_bases
|
Specificity
|
Enrichment_factor
|
SeqCap-pCancerSetA-Nov4_12 |
138,931,528 |
1,168,877,279 |
5,883,919 |
450,558,243 |
38.5% |
63
|
SeqCap-pCancerSetA-Nov4_13 |
369,134,874 |
1,424,314,151 |
21,209,194 |
614,835,055 |
43.2% |
77
|
SeqCap-pCancerSetA-Nov4_14 |
302,700,391 |
1,203,488,680 |
13,952,014 |
489,036,528 |
40.6% |
69
|
SeqCap-pCancerSetA-Nov4_15 |
277,562,818 |
1,250,329,814 |
12,577,032 |
511,943,961 |
40.9% |
70
|
SeqCap-pCancerSetA-Nov4_16 |
274,256,170 |
1,164,394,023 |
12,418,863 |
474,550,198 |
40.8% |
70
|
SeqCap-pCancerSetA-Nov4_18 |
403,128,602 |
1,170,296,929 |
23,073,184 |
461,126,140 |
39.4% |
66
|
SeqCap-pCancerSetA-Nov4_19 |
385,167,143 |
1,417,434,873 |
22,614,122 |
614,480,251 |
43.4% |
77
|
SeqCap-pCancerSetA-Nov4_2 |
354,784,810 |
1,514,708,612 |
19,490,111 |
751,025,646 |
49.6% |
99
|
SeqCap-pCancerSetA-Nov4_4 |
352,108,468 |
2,000,885,721 |
23,609,719 |
1,141,652,594 |
57.1% |
134
|
SeqCap-pCancerSetA-Nov4_5 |
196,108,966 |
1,300,234,129 |
8,246,274 |
563,004,318 |
43.3% |
77
|
SeqCap-pCancerSetA-Nov4_6 |
450,502,450 |
1,502,032,451 |
28,135,196 |
645,300,745 |
43.0% |
76
|
SeqCap-pCancerSetA-Nov4_7 |
226,755,475 |
1,432,933,860 |
10,016,683 |
629,536,922 |
43.9% |
79
|
SeqCap-pNormalSetA-Nov4_12 |
368,272,742 |
1,450,833,379 |
32,791,421 |
853,947,465 |
58.9% |
145
|
SeqCap-pNormalSetA-Nov4_13 |
330,611,335 |
1,291,478,405 |
29,764,564 |
756,289,960 |
58.6% |
143
|
SeqCap-pNormalSetA-Nov4_14 |
360,000,998 |
1,364,998,815 |
32,082,346 |
801,469,734 |
58.7% |
144
|
SeqCap-pNormalSetA-Nov4_15 |
375,193,438 |
1,970,841,697 |
30,241,737 |
1,295,408,500 |
65.7% |
194
|
SeqCap-pNormalSetA-Nov4_16 |
365,138,307 |
1,417,821,628 |
31,787,247 |
825,520,233 |
58.2% |
141
|
SeqCap-pNormalSetA-Nov4_18 |
326,952,891 |
1,305,603,890 |
28,937,598 |
760,701,025 |
58.3% |
141
|
SeqCap-pNormalSetA-Nov4_19 |
312,924,926 |
1,271,134,775 |
27,505,559 |
749,645,411 |
59.0% |
145
|
SeqCap-pNormalSetA-Nov4_2 |
353,552,883 |
1,275,196,941 |
31,331,422 |
731,603,678 |
57.4% |
136
|
SeqCap-pNormalSetA-Nov4_4 |
354,621,865 |
1,456,339,179 |
31,829,571 |
867,560,025 |
59.6% |
149
|
SeqCap-pNormalSetA-Nov4_5 |
291,891,632 |
1,066,253,299 |
27,061,797 |
618,610,388 |
58.0% |
140
|
SeqCap-pNormalSetA-Nov4_6 |
333,830,242 |
1,234,362,498 |
31,357,436 |
723,278,371 |
58.6% |
143
|
SeqCap-pNormalSetA-Nov4_7 |
377,475,888 |
1,451,628,039 |
32,325,421 |
843,343,133 |
58.1% |
140
|
|
- For some reason the specificity and enrichment factors for the second experiment is much worse than the first one.