/cemt/variants/A77952_1_lane_gembs
BACK
SAMPLE A77952_1_lane_gembs
Variant counts
| Type |
Total |
Pass |
% |
| SNPs |
1177797504 |
966841542 |
82.09 % |
| Multiallelic |
0 |
0 |
0.00 % |
VCF Filtering Stats
| Type |
#Sites |
% |
#Non-Variant Sites |
% |
#Variant Sites |
% |
| All |
1177797504 |
100% |
1156195108 |
98.17 % |
21602396 |
1.83 % |
| |
|
|
|
|
|
|
| Passed |
970193549 |
82.37 % |
963653861 |
83.35 % |
6539688 |
0.67 % |
| Filtered |
207603955 |
17.63 % |
192541247 |
16.65 % |
15062708 |
1.55 % |
| |
|
|
|
|
|
|
| q20 |
169863622 |
81.82 % |
168539341 |
87.53 % |
1324281 |
8.79 % |
| q20,qd2 |
18300252 |
8.81 % |
5631364 |
2.92 % |
12668888 |
84.11 % |
| q20,mq40 |
11194315 |
5.39 % |
11063844 |
5.75 % |
130471 |
0.87 % |
| qd2 |
2884925 |
1.39 % |
2418576 |
1.26 % |
466349 |
3.10 % |
| q20,qd2,mq40 |
2758350 |
1.33 % |
2582489 |
1.34 % |
175861 |
1.17 % |
| mq40 |
2549940 |
1.23 % |
2264434 |
1.18 % |
285506 |
1.90 % |
| qd2,mq40 |
51112 |
0.02 % |
41199 |
0.02 % |
9913 |
0.07 % |
| qd2,fs60,mq40 |
637 |
0.00 % |
0 |
0.00 % |
637 |
0.00 % |
| fs60,mq40 |
278 |
0.00 % |
0 |
0.00 % |
278 |
0.00 % |
| qd2,fs60 |
262 |
0.00 % |
0 |
0.00 % |
262 |
0.00 % |
| fs60 |
174 |
0.00 % |
0 |
0.00 % |
174 |
0.00 % |
| q20,qd2,fs60,mq40 |
46 |
0.00 % |
0 |
0.00 % |
46 |
0.00 % |
| q20,qd2,fs60 |
39 |
0.00 % |
0 |
0.00 % |
39 |
0.00 % |
| q20,fs60,mq40 |
3 |
0.00 % |
0 |
0.00 % |
3 |
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 |
8330648 |
35.59 % |
| Transition |
G>A |
All |
1042951 |
4.46 % |
| Transition |
T>C |
All |
8308000 |
35.49 % |
| Transition |
C>T |
All |
1050537 |
4.49 % |
| Transversion |
A>C |
All |
366033 |
1.56 % |
| Transversion |
C>A |
All |
1140000 |
4.87 % |
| Transversion |
T>G |
All |
366411 |
1.57 % |
| Transversion |
G>T |
All |
946669 |
4.04 % |
| Transversion |
A>T |
All |
586783 |
2.51 % |
| Transversion |
T>A |
All |
602694 |
2.57 % |
| Transversion |
C>G |
All |
336601 |
1.44 % |
| Transversion |
G>C |
All |
331142 |
1.41 % |
| |
|
|
|
|
| Transition |
A>G |
Passed |
832585 |
19.16 % |
| Transition |
G>A |
Passed |
558732 |
12.86 % |
| Transition |
T>C |
Passed |
806632 |
18.57 % |
| Transition |
C>T |
Passed |
558666 |
12.86 % |
| Transversion |
A>C |
Passed |
162740 |
3.75 % |
| Transversion |
C>A |
Passed |
353810 |
8.14 % |
| Transversion |
T>G |
Passed |
164457 |
3.79 % |
| Transversion |
G>T |
Passed |
280835 |
6.46 % |
| Transversion |
A>T |
Passed |
153190 |
3.53 % |
| Transversion |
T>A |
Passed |
160204 |
3.69 % |
| Transversion |
C>G |
Passed |
156755 |
3.61 % |
| Transversion |
G>C |
Passed |
156028 |
3.59 % |
| |
|
|
|
|
| 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 |
4.01 |
18732136 |
4676333 |
| Passed |
1.74 |
2756615 |
1588019 |
| dbSNPAll |
0 |
0 |
0 |
| dbSNPPassed |
0 |
0 |
0 |