/CEMT/variants/A75625_1_lane_gembs
BACK
SAMPLE A75625_1_lane_gembs
Variant counts
| Type |
Total |
Pass |
% |
| SNPs |
1176449016 |
1059515934 |
90.06 % |
| Multiallelic |
0 |
0 |
0.00 % |
VCF Filtering Stats
| Type |
#Sites |
% |
#Non-Variant Sites |
% |
#Variant Sites |
% |
| All |
1176449016 |
100% |
1158551321 |
98.48 % |
17897695 |
1.52 % |
| |
|
|
|
|
|
|
| Passed |
1061234793 |
90.21 % |
1056034377 |
91.15 % |
5200416 |
0.49 % |
| Filtered |
115214223 |
9.79 % |
102516944 |
8.85 % |
12697279 |
1.20 % |
| |
|
|
|
|
|
|
| q20 |
80039785 |
69.47 % |
79107747 |
77.17 % |
932038 |
7.34 % |
| q20,qd2 |
13907834 |
12.07 % |
3498001 |
3.41 % |
10409833 |
81.98 % |
| q20,mq40 |
11970874 |
10.39 % |
11819288 |
11.53 % |
151586 |
1.19 % |
| mq40 |
3789352 |
3.29 % |
3484432 |
3.40 % |
304920 |
2.40 % |
| qd2 |
2839704 |
2.46 % |
2156128 |
2.10 % |
683576 |
5.38 % |
| q20,qd2,mq40 |
2602613 |
2.26 % |
2400510 |
2.34 % |
202103 |
1.59 % |
| qd2,mq40 |
62403 |
0.05 % |
50838 |
0.05 % |
11565 |
0.09 % |
| qd2,fs60,mq40 |
743 |
0.00 % |
0 |
0.00 % |
743 |
0.01 % |
| fs60,mq40 |
314 |
0.00 % |
0 |
0.00 % |
314 |
0.00 % |
| qd2,fs60 |
298 |
0.00 % |
0 |
0.00 % |
298 |
0.00 % |
| fs60 |
177 |
0.00 % |
0 |
0.00 % |
177 |
0.00 % |
| q20,qd2,fs60 |
60 |
0.00 % |
0 |
0.00 % |
60 |
0.00 % |
| q20,qd2,fs60,mq40 |
60 |
0.00 % |
0 |
0.00 % |
60 |
0.00 % |
| q20,fs60,mq40 |
6 |
0.00 % |
0 |
0.00 % |
6 |
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 |
7083747 |
36.11 % |
| Transition |
G>A |
All |
968533 |
4.94 % |
| Transition |
T>C |
All |
7267135 |
37.04 % |
| Transition |
C>T |
All |
977170 |
4.98 % |
| Transversion |
A>C |
All |
348803 |
1.78 % |
| Transversion |
C>A |
All |
519659 |
2.65 % |
| Transversion |
T>G |
All |
351923 |
1.79 % |
| Transversion |
G>T |
All |
503756 |
2.57 % |
| Transversion |
A>T |
All |
481355 |
2.45 % |
| Transversion |
T>A |
All |
492415 |
2.51 % |
| Transversion |
C>G |
All |
313615 |
1.60 % |
| Transversion |
G>C |
All |
311641 |
1.59 % |
| |
|
|
|
|
| Transition |
A>G |
Passed |
1037615 |
22.05 % |
| Transition |
G>A |
Passed |
636445 |
13.52 % |
| Transition |
T>C |
Passed |
1003730 |
21.33 % |
| Transition |
C>T |
Passed |
636164 |
13.52 % |
| Transversion |
A>C |
Passed |
181332 |
3.85 % |
| Transversion |
C>A |
Passed |
186997 |
3.97 % |
| Transversion |
T>G |
Passed |
183101 |
3.89 % |
| Transversion |
G>T |
Passed |
177773 |
3.78 % |
| Transversion |
A>T |
Passed |
152933 |
3.25 % |
| Transversion |
T>A |
Passed |
155850 |
3.31 % |
| Transversion |
C>G |
Passed |
177467 |
3.77 % |
| Transversion |
G>C |
Passed |
176798 |
3.76 % |
| |
|
|
|
|
| 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 |
4.90 |
16296585 |
3323167 |
| Passed |
2.38 |
3313954 |
1392251 |
| dbSNPAll |
0 |
0 |
0 |
| dbSNPPassed |
0 |
0 |
0 |