/cemt/variants/A54776_3_lane_gembs
BACK
SAMPLE A54776_3_lane_gembs
Variant counts
| Type |
Total |
Pass |
% |
| SNPs |
1162513537 |
765040963 |
65.81 % |
| Multiallelic |
0 |
0 |
0.00 % |
VCF Filtering Stats
| Type |
#Sites |
% |
#Non-Variant Sites |
% |
#Variant Sites |
% |
| All |
1162513537 |
100% |
1141548205 |
98.20 % |
20965332 |
1.80 % |
| |
|
|
|
|
|
|
| Passed |
768056762 |
66.07 % |
762611353 |
66.81 % |
5445409 |
0.71 % |
| Filtered |
394456775 |
33.93 % |
378936852 |
33.19 % |
15519923 |
2.02 % |
| |
|
|
|
|
|
|
| q20 |
350214682 |
88.78 % |
346363043 |
91.40 % |
3851639 |
24.82 % |
| q20,qd2 |
21218891 |
5.38 % |
10329237 |
2.73 % |
10889654 |
70.17 % |
| q20,mq40 |
10850037 |
2.75 % |
10668312 |
2.82 % |
181725 |
1.17 % |
| qd2 |
7209092 |
1.83 % |
6995196 |
1.85 % |
213896 |
1.38 % |
| q20,qd2,mq40 |
3113132 |
0.79 % |
2914141 |
0.77 % |
198991 |
1.28 % |
| mq40 |
1783253 |
0.45 % |
1617252 |
0.43 % |
166001 |
1.07 % |
| qd2,mq40 |
59922 |
0.02 % |
49671 |
0.01 % |
10251 |
0.07 % |
| q20,qd2,fs60 |
2270 |
0.00 % |
0 |
0.00 % |
2270 |
0.01 % |
| qd2,fs60 |
1863 |
0.00 % |
0 |
0.00 % |
1863 |
0.01 % |
| fs60 |
1821 |
0.00 % |
0 |
0.00 % |
1821 |
0.01 % |
| qd2,fs60,mq40 |
1307 |
0.00 % |
0 |
0.00 % |
1307 |
0.01 % |
| fs60,mq40 |
365 |
0.00 % |
0 |
0.00 % |
365 |
0.00 % |
| q20,qd2,fs60,mq40 |
135 |
0.00 % |
0 |
0.00 % |
135 |
0.00 % |
| q20,fs60 |
5 |
0.00 % |
0 |
0.00 % |
5 |
0.00 % |
| q20,fs60,mq40 |
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 |
7892252 |
34.15 % |
| Transition |
G>A |
All |
1673723 |
7.24 % |
| Transition |
T>C |
All |
6187598 |
26.78 % |
| Transition |
C>T |
All |
1853280 |
8.02 % |
| Transversion |
A>C |
All |
387071 |
1.67 % |
| Transversion |
C>A |
All |
994163 |
4.30 % |
| Transversion |
T>G |
All |
470689 |
2.04 % |
| Transversion |
G>T |
All |
943803 |
4.08 % |
| Transversion |
A>T |
All |
943151 |
4.08 % |
| Transversion |
T>A |
All |
996668 |
4.31 % |
| Transversion |
C>G |
All |
427687 |
1.85 % |
| Transversion |
G>C |
All |
339277 |
1.47 % |
| |
|
|
|
|
| Transition |
A>G |
Passed |
651501 |
19.63 % |
| Transition |
G>A |
Passed |
499221 |
15.04 % |
| Transition |
T>C |
Passed |
584517 |
17.61 % |
| Transition |
C>T |
Passed |
505452 |
15.23 % |
| Transversion |
A>C |
Passed |
136595 |
4.12 % |
| Transversion |
C>A |
Passed |
141389 |
4.26 % |
| Transversion |
T>G |
Passed |
140742 |
4.24 % |
| Transversion |
G>T |
Passed |
142118 |
4.28 % |
| Transversion |
A>T |
Passed |
129262 |
3.90 % |
| Transversion |
T>A |
Passed |
130001 |
3.92 % |
| Transversion |
C>G |
Passed |
129632 |
3.91 % |
| Transversion |
G>C |
Passed |
128133 |
3.86 % |
| |
|
|
|
|
| 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 |
3.20 |
17606853 |
5502509 |
| Passed |
2.08 |
2240691 |
1077872 |
| dbSNPAll |
0 |
0 |
0 |
| dbSNPPassed |
0 |
0 |
0 |