/cemt/variants/K005720_0_lane_gembs
BACK
SAMPLE K005720_0_lane_gembs
Variant counts
| Type |
Total |
Pass |
% |
| SNPs |
1176256056 |
938796132 |
79.81 % |
| Multiallelic |
0 |
0 |
0.00 % |
VCF Filtering Stats
| Type |
#Sites |
% |
#Non-Variant Sites |
% |
#Variant Sites |
% |
| All |
1176256056 |
100% |
1156126003 |
98.29 % |
20130053 |
1.71 % |
| |
|
|
|
|
|
|
| Passed |
941371587 |
80.03 % |
935849343 |
80.95 % |
5522244 |
0.59 % |
| Filtered |
234884469 |
19.97 % |
220276660 |
19.05 % |
14607809 |
1.55 % |
| |
|
|
|
|
|
|
| q20 |
196541881 |
83.68 % |
194774100 |
88.42 % |
1767781 |
12.10 % |
| q20,qd2 |
17321794 |
7.37 % |
5552222 |
2.52 % |
11769572 |
80.57 % |
| q20,mq40 |
12689398 |
5.40 % |
12501455 |
5.68 % |
187943 |
1.29 % |
| mq40 |
3490455 |
1.49 % |
3195038 |
1.45 % |
295417 |
2.02 % |
| q20,qd2,mq40 |
2932098 |
1.25 % |
2700605 |
1.23 % |
231493 |
1.58 % |
| qd2 |
1861469 |
0.79 % |
1516764 |
0.69 % |
344705 |
2.36 % |
| qd2,mq40 |
46213 |
0.02 % |
36476 |
0.02 % |
9737 |
0.07 % |
| qd2,fs60,mq40 |
571 |
0.00 % |
0 |
0.00 % |
571 |
0.00 % |
| qd2,fs60 |
271 |
0.00 % |
0 |
0.00 % |
271 |
0.00 % |
| fs60,mq40 |
181 |
0.00 % |
0 |
0.00 % |
181 |
0.00 % |
| fs60 |
82 |
0.00 % |
0 |
0.00 % |
82 |
0.00 % |
| q20,qd2,fs60,mq40 |
34 |
0.00 % |
0 |
0.00 % |
34 |
0.00 % |
| q20,qd2,fs60 |
18 |
0.00 % |
0 |
0.00 % |
18 |
0.00 % |
| q20,fs60,mq40 |
4 |
0.00 % |
0 |
0.00 % |
4 |
0.00 % |
| q20,fs60 |
0 |
0.00 % |
0 |
0.00 % |
0 |
0.00 % |
Coverage and Quality
| Coverage Variants |
Quality Variants |
 |
 |
Filtering Criteria Distribution
| Phred scale strand bias estimated using Fisher's Exact Test. |
 |
| Allele-specific call confidence normalized by depth of sample reads supporting the allele. Variants. |
Allele-specific call confidence normalized by depth of sample reads supporting the allele. Non-Variants. |
 |
 |
| Root Mean Square of the mapping quality of reads. Variants. |
Root Mean Square of the mapping quality of reads. Non-Variants. |
 |
 |
Mutations
| Type |
Mutation |
Status |
# |
% |
| Transition |
A>G |
All |
7906848 |
36.12 % |
| Transition |
G>A |
All |
1094557 |
5.00 % |
| Transition |
T>C |
All |
7199456 |
32.89 % |
| Transition |
C>T |
All |
1209390 |
5.53 % |
| Transversion |
A>C |
All |
506672 |
2.31 % |
| Transversion |
C>A |
All |
747941 |
3.42 % |
| Transversion |
T>G |
All |
541698 |
2.47 % |
| Transversion |
G>T |
All |
729007 |
3.33 % |
| Transversion |
A>T |
All |
485591 |
2.22 % |
| Transversion |
T>A |
All |
507255 |
2.32 % |
| Transversion |
C>G |
All |
491177 |
2.24 % |
| Transversion |
G>C |
All |
468502 |
2.14 % |
| |
|
|
|
|
| Transition |
A>G |
Passed |
797147 |
19.61 % |
| Transition |
G>A |
Passed |
582465 |
14.33 % |
| Transition |
T>C |
Passed |
781151 |
19.21 % |
| Transition |
C>T |
Passed |
589906 |
14.51 % |
| Transversion |
A>C |
Passed |
166696 |
4.10 % |
| Transversion |
C>A |
Passed |
175199 |
4.31 % |
| Transversion |
T>G |
Passed |
168838 |
4.15 % |
| Transversion |
G>T |
Passed |
173704 |
4.27 % |
| Transversion |
A>T |
Passed |
149821 |
3.68 % |
| Transversion |
T>A |
Passed |
150489 |
3.70 % |
| Transversion |
C>G |
Passed |
165737 |
4.08 % |
| Transversion |
G>C |
Passed |
164716 |
4.05 % |
| |
|
|
|
|
| Transition |
A>G |
dbSNPAll |
0 |
0.00 % |
| Transition |
G>A |
dbSNPAll |
0 |
0.00 % |
| Transition |
T>C |
dbSNPAll |
0 |
0.00 % |
| Transition |
C>T |
dbSNPAll |
0 |
0.00 % |
| Transversion |
A>C |
dbSNPAll |
0 |
0.00 % |
| Transversion |
C>A |
dbSNPAll |
0 |
0.00 % |
| Transversion |
T>G |
dbSNPAll |
0 |
0.00 % |
| Transversion |
G>T |
dbSNPAll |
0 |
0.00 % |
| Transversion |
A>T |
dbSNPAll |
0 |
0.00 % |
| Transversion |
T>A |
dbSNPAll |
0 |
0.00 % |
| Transversion |
C>G |
dbSNPAll |
0 |
0.00 % |
| Transversion |
G>C |
dbSNPAll |
0 |
0.00 % |
| |
|
|
|
|
| Transition |
A>G |
dbSNPPassed |
0 |
0.00 % |
| Transition |
G>A |
dbSNPPassed |
0 |
0.00 % |
| Transition |
T>C |
dbSNPPassed |
0 |
0.00 % |
| Transition |
C>T |
dbSNPPassed |
0 |
0.00 % |
| Transversion |
A>C |
dbSNPPassed |
0 |
0.00 % |
| Transversion |
C>A |
dbSNPPassed |
0 |
0.00 % |
| Transversion |
T>G |
dbSNPPassed |
0 |
0.00 % |
| Transversion |
G>T |
dbSNPPassed |
0 |
0.00 % |
| Transversion |
A>T |
dbSNPPassed |
0 |
0.00 % |
| Transversion |
T>A |
dbSNPPassed |
0 |
0.00 % |
| Transversion |
C>G |
dbSNPPassed |
0 |
0.00 % |
| Transversion |
G>C |
dbSNPPassed |
0 |
0.00 % |
| |
|
|
|
|
Ti/Tv Ratio
| Status |
Ratio |
Transitions |
Transversions |
| All |
3.89 |
17410251 |
4477843 |
| Passed |
2.09 |
2750669 |
1315200 |
| dbSNPAll |
0 |
0 |
0 |
| dbSNPPassed |
0 |
0 |
0 |