/cemt/variants/A77947_1_lane_gembs
BACK
SAMPLE A77947_1_lane_gembs
Variant counts
| Type |
Total |
Pass |
% |
| SNPs |
1176197956 |
1021410530 |
86.84 % |
| Multiallelic |
0 |
0 |
0.00 % |
VCF Filtering Stats
| Type |
#Sites |
% |
#Non-Variant Sites |
% |
#Variant Sites |
% |
| All |
1176197956 |
100% |
1157185409 |
98.38 % |
19012547 |
1.62 % |
| |
|
|
|
|
|
|
| Passed |
1023823855 |
87.05 % |
1018175760 |
87.99 % |
5648095 |
0.55 % |
| Filtered |
152374101 |
12.95 % |
139009649 |
12.01 % |
13364452 |
1.31 % |
| |
|
|
|
|
|
|
| q20 |
117587761 |
77.17 % |
116612774 |
83.89 % |
974987 |
7.30 % |
| q20,qd2 |
15684835 |
10.29 % |
4425547 |
3.18 % |
11259288 |
84.25 % |
| q20,mq40 |
10954116 |
7.19 % |
10825334 |
7.79 % |
128782 |
0.96 % |
| qd2 |
2785269 |
1.83 % |
2250623 |
1.62 % |
534646 |
4.00 % |
| q20,qd2,mq40 |
2691409 |
1.77 % |
2520691 |
1.81 % |
170718 |
1.28 % |
| mq40 |
2614036 |
1.72 % |
2329877 |
1.68 % |
284159 |
2.13 % |
| qd2,mq40 |
55209 |
0.04 % |
44803 |
0.03 % |
10406 |
0.08 % |
| qd2,fs60,mq40 |
634 |
0.00 % |
0 |
0.00 % |
634 |
0.00 % |
| fs60,mq40 |
301 |
0.00 % |
0 |
0.00 % |
301 |
0.00 % |
| qd2,fs60 |
256 |
0.00 % |
0 |
0.00 % |
256 |
0.00 % |
| fs60 |
183 |
0.00 % |
0 |
0.00 % |
183 |
0.00 % |
| q20,qd2,fs60,mq40 |
56 |
0.00 % |
0 |
0.00 % |
56 |
0.00 % |
| q20,qd2,fs60 |
35 |
0.00 % |
0 |
0.00 % |
35 |
0.00 % |
| q20,fs60 |
1 |
0.00 % |
0 |
0.00 % |
1 |
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 |
7418371 |
35.74 % |
| Transition |
G>A |
All |
953672 |
4.59 % |
| Transition |
T>C |
All |
7398030 |
35.64 % |
| Transition |
C>T |
All |
958976 |
4.62 % |
| Transversion |
A>C |
All |
334267 |
1.61 % |
| Transversion |
C>A |
All |
921441 |
4.44 % |
| Transversion |
T>G |
All |
336866 |
1.62 % |
| Transversion |
G>T |
All |
770876 |
3.71 % |
| Transversion |
A>T |
All |
526152 |
2.53 % |
| Transversion |
T>A |
All |
544469 |
2.62 % |
| Transversion |
C>G |
All |
300210 |
1.45 % |
| Transversion |
G>C |
All |
294752 |
1.42 % |
| |
|
|
|
|
| Transition |
A>G |
Passed |
869179 |
19.59 % |
| Transition |
G>A |
Passed |
586720 |
13.23 % |
| Transition |
T>C |
Passed |
828037 |
18.67 % |
| Transition |
C>T |
Passed |
584395 |
13.17 % |
| Transversion |
A>C |
Passed |
168675 |
3.80 % |
| Transversion |
C>A |
Passed |
325682 |
7.34 % |
| Transversion |
T>G |
Passed |
171084 |
3.86 % |
| Transversion |
G>T |
Passed |
262989 |
5.93 % |
| Transversion |
A>T |
Passed |
153318 |
3.46 % |
| Transversion |
T>A |
Passed |
161256 |
3.63 % |
| Transversion |
C>G |
Passed |
163179 |
3.68 % |
| Transversion |
G>C |
Passed |
161778 |
3.65 % |
| |
|
|
|
|
| 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 |
4.15 |
16729049 |
4029033 |
| Passed |
1.83 |
2868331 |
1567961 |
| dbSNPAll |
0 |
0 |
0 |
| dbSNPPassed |
0 |
0 |
0 |