/cemt/variants/A59696_3_lane_gembs
BACK
SAMPLE A59696_3_lane_gembs
Variant counts
| Type |
Total |
Pass |
% |
| SNPs |
1159459947 |
1051318539 |
90.67 % |
| Multiallelic |
0 |
0 |
0.00 % |
VCF Filtering Stats
| Type |
#Sites |
% |
#Non-Variant Sites |
% |
#Variant Sites |
% |
| All |
1159459947 |
100% |
1147320802 |
98.95 % |
12139145 |
1.05 % |
| |
|
|
|
|
|
|
| Passed |
1051932853 |
90.73 % |
1048256864 |
91.37 % |
3675989 |
0.35 % |
| Filtered |
107527094 |
9.27 % |
99063938 |
8.63 % |
8463156 |
0.80 % |
| |
|
|
|
|
|
|
| q20 |
71750120 |
66.73 % |
70679355 |
71.35 % |
1070765 |
12.65 % |
| q20,qd2 |
11672349 |
10.86 % |
5468416 |
5.52 % |
6203933 |
73.31 % |
| q20,mq40 |
11561550 |
10.75 % |
11299488 |
11.41 % |
262062 |
3.10 % |
| qd2 |
6115877 |
5.69 % |
5775073 |
5.83 % |
340804 |
4.03 % |
| q20,qd2,mq40 |
3205785 |
2.98 % |
2881010 |
2.91 % |
324775 |
3.84 % |
| mq40 |
3148236 |
2.93 % |
2903291 |
2.93 % |
244945 |
2.89 % |
| qd2,mq40 |
69167 |
0.06 % |
57305 |
0.06 % |
11862 |
0.14 % |
| qd2,fs60,mq40 |
1081 |
0.00 % |
0 |
0.00 % |
1081 |
0.01 % |
| q20,qd2,fs60 |
910 |
0.00 % |
0 |
0.00 % |
910 |
0.01 % |
| fs60 |
903 |
0.00 % |
0 |
0.00 % |
903 |
0.01 % |
| qd2,fs60 |
577 |
0.00 % |
0 |
0.00 % |
577 |
0.01 % |
| fs60,mq40 |
414 |
0.00 % |
0 |
0.00 % |
414 |
0.00 % |
| q20,qd2,fs60,mq40 |
112 |
0.00 % |
0 |
0.00 % |
112 |
0.00 % |
| q20,fs60,mq40 |
8 |
0.00 % |
0 |
0.00 % |
8 |
0.00 % |
| q20,fs60 |
5 |
0.00 % |
0 |
0.00 % |
5 |
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 |
3301723 |
23.73 % |
| Transition |
G>A |
All |
1145628 |
8.23 % |
| Transition |
T>C |
All |
3297014 |
23.70 % |
| Transition |
C>T |
All |
1147838 |
8.25 % |
| Transversion |
A>C |
All |
434326 |
3.12 % |
| Transversion |
C>A |
All |
848922 |
6.10 % |
| Transversion |
T>G |
All |
431717 |
3.10 % |
| Transversion |
G>T |
All |
872973 |
6.27 % |
| Transversion |
A>T |
All |
909995 |
6.54 % |
| Transversion |
T>A |
All |
880016 |
6.32 % |
| Transversion |
C>G |
All |
320695 |
2.30 % |
| Transversion |
G>C |
All |
323092 |
2.32 % |
| |
|
|
|
|
| Transition |
A>G |
Passed |
700692 |
16.36 % |
| Transition |
G>A |
Passed |
651571 |
15.22 % |
| Transition |
T>C |
Passed |
705288 |
16.47 % |
| Transition |
C>T |
Passed |
652795 |
15.24 % |
| Transversion |
A>C |
Passed |
201140 |
4.70 % |
| Transversion |
C>A |
Passed |
222186 |
5.19 % |
| Transversion |
T>G |
Passed |
199828 |
4.67 % |
| Transversion |
G>T |
Passed |
219931 |
5.14 % |
| Transversion |
A>T |
Passed |
196333 |
4.58 % |
| Transversion |
T>A |
Passed |
196277 |
4.58 % |
| Transversion |
C>G |
Passed |
167514 |
3.91 % |
| Transversion |
G>C |
Passed |
168542 |
3.94 % |
| |
|
|
|
|
| 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 |
1.77 |
8892203 |
5021736 |
| Passed |
1.72 |
2710346 |
1571751 |
| dbSNPAll |
0 |
0 |
0 |
| dbSNPPassed |
0 |
0 |
0 |