/cemt/variants/A75618_1_lane_gembs
BACK
SAMPLE A75618_1_lane_gembs
Variant counts
| Type |
Total |
Pass |
% |
| SNPs |
1170947661 |
996094890 |
85.07 % |
| Multiallelic |
0 |
0 |
0.00 % |
VCF Filtering Stats
| Type |
#Sites |
% |
#Non-Variant Sites |
% |
#Variant Sites |
% |
| All |
1170947661 |
100% |
1151684703 |
98.35 % |
19262958 |
1.65 % |
| |
|
|
|
|
|
|
| Passed |
998728660 |
85.29 % |
992810858 |
86.21 % |
5917802 |
0.59 % |
| Filtered |
172219001 |
14.71 % |
158873845 |
13.79 % |
13345156 |
1.34 % |
| |
|
|
|
|
|
|
| q20 |
138853852 |
80.63 % |
137845327 |
86.76 % |
1008525 |
7.56 % |
| q20,qd2 |
14940481 |
8.68 % |
3621574 |
2.28 % |
11318907 |
84.82 % |
| q20,mq40 |
11124006 |
6.46 % |
11012355 |
6.93 % |
111651 |
0.84 % |
| mq40 |
2705814 |
1.57 % |
2449238 |
1.54 % |
256576 |
1.92 % |
| q20,qd2,mq40 |
2561717 |
1.49 % |
2407970 |
1.52 % |
153747 |
1.15 % |
| qd2 |
1982377 |
1.15 % |
1497495 |
0.94 % |
484882 |
3.63 % |
| qd2,mq40 |
49089 |
0.03 % |
39886 |
0.03 % |
9203 |
0.07 % |
| qd2,fs60,mq40 |
763 |
0.00 % |
0 |
0.00 % |
763 |
0.01 % |
| qd2,fs60 |
320 |
0.00 % |
0 |
0.00 % |
320 |
0.00 % |
| fs60,mq40 |
270 |
0.00 % |
0 |
0.00 % |
270 |
0.00 % |
| fs60 |
178 |
0.00 % |
0 |
0.00 % |
178 |
0.00 % |
| q20,qd2,fs60 |
66 |
0.00 % |
0 |
0.00 % |
66 |
0.00 % |
| q20,qd2,fs60,mq40 |
66 |
0.00 % |
0 |
0.00 % |
66 |
0.00 % |
| q20,fs60,mq40 |
2 |
0.00 % |
0 |
0.00 % |
2 |
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 |
7843630 |
37.48 % |
| Transition |
G>A |
All |
949469 |
4.54 % |
| Transition |
T>C |
All |
7909877 |
37.79 % |
| Transition |
C>T |
All |
951533 |
4.55 % |
| Transversion |
A>C |
All |
342246 |
1.64 % |
| Transversion |
C>A |
All |
506932 |
2.42 % |
| Transversion |
T>G |
All |
346240 |
1.65 % |
| Transversion |
G>T |
All |
489538 |
2.34 % |
| Transversion |
A>T |
All |
478074 |
2.28 % |
| Transversion |
T>A |
All |
494535 |
2.36 % |
| Transversion |
C>G |
All |
310083 |
1.48 % |
| Transversion |
G>C |
All |
306784 |
1.47 % |
| |
|
|
|
|
| Transition |
A>G |
Passed |
939543 |
21.26 % |
| Transition |
G>A |
Passed |
595485 |
13.48 % |
| Transition |
T>C |
Passed |
931308 |
21.08 % |
| Transition |
C>T |
Passed |
597182 |
13.52 % |
| Transversion |
A>C |
Passed |
176939 |
4.00 % |
| Transversion |
C>A |
Passed |
182664 |
4.13 % |
| Transversion |
T>G |
Passed |
178758 |
4.05 % |
| Transversion |
G>T |
Passed |
172939 |
3.91 % |
| Transversion |
A>T |
Passed |
152750 |
3.46 % |
| Transversion |
T>A |
Passed |
157206 |
3.56 % |
| Transversion |
C>G |
Passed |
167465 |
3.79 % |
| Transversion |
G>C |
Passed |
166242 |
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 |
5.39 |
17654509 |
3274432 |
| Passed |
2.26 |
3063518 |
1354963 |
| dbSNPAll |
0 |
0 |
0 |
| dbSNPPassed |
0 |
0 |
0 |