/cemt/variants/A54771_3_lane_gembs
BACK
SAMPLE A54771_3_lane_gembs
Variant counts
| Type |
Total |
Pass |
% |
| SNPs |
1161295070 |
666038176 |
57.35 % |
| Multiallelic |
0 |
0 |
0.00 % |
VCF Filtering Stats
| Type |
#Sites |
% |
#Non-Variant Sites |
% |
#Variant Sites |
% |
| All |
1161295070 |
100% |
1137715065 |
97.97 % |
23580005 |
2.03 % |
| |
|
|
|
|
|
|
| Passed |
669584734 |
57.66 % |
663855007 |
58.35 % |
5729727 |
0.86 % |
| Filtered |
491710336 |
42.34 % |
473860058 |
41.65 % |
17850278 |
2.67 % |
| |
|
|
|
|
|
|
| q20 |
437776076 |
89.03 % |
432760524 |
91.33 % |
5015552 |
28.10 % |
| q20,qd2 |
26806380 |
5.45 % |
14826026 |
3.13 % |
11980354 |
67.12 % |
| q20,mq40 |
11478894 |
2.33 % |
11265594 |
2.38 % |
213300 |
1.19 % |
| qd2 |
10339966 |
2.10 % |
10126076 |
2.14 % |
213890 |
1.20 % |
| q20,qd2,mq40 |
3493873 |
0.71 % |
3265903 |
0.69 % |
227970 |
1.28 % |
| mq40 |
1734722 |
0.35 % |
1560604 |
0.33 % |
174118 |
0.98 % |
| qd2,mq40 |
66178 |
0.01 % |
55331 |
0.01 % |
10847 |
0.06 % |
| q20,qd2,fs60 |
4420 |
0.00 % |
0 |
0.00 % |
4420 |
0.02 % |
| fs60 |
4281 |
0.00 % |
0 |
0.00 % |
4281 |
0.02 % |
| qd2,fs60 |
3614 |
0.00 % |
0 |
0.00 % |
3614 |
0.02 % |
| qd2,fs60,mq40 |
1312 |
0.00 % |
0 |
0.00 % |
1312 |
0.01 % |
| fs60,mq40 |
414 |
0.00 % |
0 |
0.00 % |
414 |
0.00 % |
| q20,qd2,fs60,mq40 |
196 |
0.00 % |
0 |
0.00 % |
196 |
0.00 % |
| q20,fs60 |
9 |
0.00 % |
0 |
0.00 % |
9 |
0.00 % |
| q20,fs60,mq40 |
1 |
0.00 % |
0 |
0.00 % |
1 |
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 |
8297587 |
31.58 % |
| Transition |
G>A |
All |
2120586 |
8.07 % |
| Transition |
T>C |
All |
6240615 |
23.75 % |
| Transition |
C>T |
All |
2256871 |
8.59 % |
| Transversion |
A>C |
All |
448160 |
1.71 % |
| Transversion |
C>A |
All |
1545789 |
5.88 % |
| Transversion |
T>G |
All |
559279 |
2.13 % |
| Transversion |
G>T |
All |
1464985 |
5.58 % |
| Transversion |
A>T |
All |
1185133 |
4.51 % |
| Transversion |
T>A |
All |
1262629 |
4.80 % |
| Transversion |
C>G |
All |
503019 |
1.91 % |
| Transversion |
G>C |
All |
392759 |
1.49 % |
| |
|
|
|
|
| Transition |
A>G |
Passed |
599848 |
19.71 % |
| Transition |
G>A |
Passed |
452616 |
14.87 % |
| Transition |
T>C |
Passed |
524496 |
17.23 % |
| Transition |
C>T |
Passed |
457655 |
15.03 % |
| Transversion |
A>C |
Passed |
122585 |
4.03 % |
| Transversion |
C>A |
Passed |
138276 |
4.54 % |
| Transversion |
T>G |
Passed |
126749 |
4.16 % |
| Transversion |
G>T |
Passed |
137098 |
4.50 % |
| Transversion |
A>T |
Passed |
124328 |
4.08 % |
| Transversion |
T>A |
Passed |
125492 |
4.12 % |
| Transversion |
C>G |
Passed |
118838 |
3.90 % |
| Transversion |
G>C |
Passed |
116004 |
3.81 % |
| |
|
|
|
|
| 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 |
2.57 |
18915659 |
7361753 |
| Passed |
2.02 |
2034615 |
1009370 |
| dbSNPAll |
0 |
0 |
0 |
| dbSNPPassed |
0 |
0 |
0 |