/cemt/variants/A36008_3_lane_gembs
BACK
SAMPLE A36008_3_lane_gembs
Variant counts
| Type |
Total |
Pass |
% |
| SNPs |
1167320005 |
913475574 |
78.25 % |
| Multiallelic |
0 |
0 |
0.00 % |
VCF Filtering Stats
| Type |
#Sites |
% |
#Non-Variant Sites |
% |
#Variant Sites |
% |
| All |
1167320005 |
100% |
1150299381 |
98.54 % |
17020624 |
1.46 % |
| |
|
|
|
|
|
|
| Passed |
915131993 |
78.40 % |
910872908 |
79.19 % |
4259085 |
0.47 % |
| Filtered |
252188012 |
21.60 % |
239426473 |
20.81 % |
12761539 |
1.39 % |
| |
|
|
|
|
|
|
| q20 |
209420537 |
83.04 % |
206956957 |
86.44 % |
2463580 |
19.30 % |
| q20,qd2 |
18561048 |
7.36 % |
9244156 |
3.86 % |
9316892 |
73.01 % |
| q20,mq40 |
12162695 |
4.82 % |
11902913 |
4.97 % |
259782 |
2.04 % |
| qd2 |
6089727 |
2.41 % |
5865549 |
2.45 % |
224178 |
1.76 % |
| q20,qd2,mq40 |
3201445 |
1.27 % |
2917355 |
1.22 % |
284090 |
2.23 % |
| mq40 |
2671625 |
1.06 % |
2475887 |
1.03 % |
195738 |
1.53 % |
| qd2,mq40 |
75217 |
0.03 % |
63656 |
0.03 % |
11561 |
0.09 % |
| fs60 |
1588 |
0.00 % |
0 |
0.00 % |
1588 |
0.01 % |
| qd2,fs60,mq40 |
1251 |
0.00 % |
0 |
0.00 % |
1251 |
0.01 % |
| qd2,fs60 |
1215 |
0.00 % |
0 |
0.00 % |
1215 |
0.01 % |
| q20,qd2,fs60 |
1176 |
0.00 % |
0 |
0.00 % |
1176 |
0.01 % |
| fs60,mq40 |
351 |
0.00 % |
0 |
0.00 % |
351 |
0.00 % |
| q20,qd2,fs60,mq40 |
129 |
0.00 % |
0 |
0.00 % |
129 |
0.00 % |
| q20,fs60 |
7 |
0.00 % |
0 |
0.00 % |
7 |
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 |
5618757 |
29.66 % |
| Transition |
G>A |
All |
1497370 |
7.90 % |
| Transition |
T>C |
All |
5419299 |
28.61 % |
| Transition |
C>T |
All |
1513481 |
7.99 % |
| Transversion |
A>C |
All |
395347 |
2.09 % |
| Transversion |
C>A |
All |
855348 |
4.52 % |
| Transversion |
T>G |
All |
406976 |
2.15 % |
| Transversion |
G>T |
All |
853767 |
4.51 % |
| Transversion |
A>T |
All |
855192 |
4.51 % |
| Transversion |
T>A |
All |
866042 |
4.57 % |
| Transversion |
C>G |
All |
335068 |
1.77 % |
| Transversion |
G>C |
All |
327756 |
1.73 % |
| |
|
|
|
|
| Transition |
A>G |
Passed |
661131 |
17.93 % |
| Transition |
G>A |
Passed |
572381 |
15.53 % |
| Transition |
T>C |
Passed |
657737 |
17.84 % |
| Transition |
C>T |
Passed |
573174 |
15.55 % |
| Transversion |
A>C |
Passed |
153708 |
4.17 % |
| Transversion |
C>A |
Passed |
163579 |
4.44 % |
| Transversion |
T>G |
Passed |
154077 |
4.18 % |
| Transversion |
G>T |
Passed |
163434 |
4.43 % |
| Transversion |
A>T |
Passed |
148793 |
4.04 % |
| Transversion |
T>A |
Passed |
149999 |
4.07 % |
| Transversion |
C>G |
Passed |
144156 |
3.91 % |
| Transversion |
G>C |
Passed |
144106 |
3.91 % |
| |
|
|
|
|
| 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 |
2.87 |
14048907 |
4895496 |
| Passed |
2.02 |
2464423 |
1221852 |
| dbSNPAll |
0 |
0 |
0 |
| dbSNPPassed |
0 |
0 |
0 |