/cemt/variants/A36003_3_lane_gembs
BACK
SAMPLE A36003_3_lane_gembs
Variant counts
| Type |
Total |
Pass |
% |
| SNPs |
1165470881 |
793605116 |
68.09 % |
| Multiallelic |
0 |
0 |
0.00 % |
VCF Filtering Stats
| Type |
#Sites |
% |
#Non-Variant Sites |
% |
#Variant Sites |
% |
| All |
1165470881 |
100% |
1147484371 |
98.46 % |
17986510 |
1.54 % |
| |
|
|
|
|
|
|
| Passed |
795855718 |
68.29 % |
791232023 |
68.95 % |
4623695 |
0.58 % |
| Filtered |
369615163 |
31.71 % |
356252348 |
31.05 % |
13362815 |
1.68 % |
| |
|
|
|
|
|
|
| q20 |
326554889 |
88.35 % |
323301717 |
90.75 % |
3253172 |
24.34 % |
| q20,qd2 |
20489834 |
5.54 % |
11273970 |
3.16 % |
9215864 |
68.97 % |
| q20,mq40 |
12030245 |
3.25 % |
11787484 |
3.31 % |
242761 |
1.82 % |
| qd2 |
4874745 |
1.32 % |
4676957 |
1.31 % |
197788 |
1.48 % |
| q20,qd2,mq40 |
3187035 |
0.86 % |
2929581 |
0.82 % |
257454 |
1.93 % |
| mq40 |
2400962 |
0.65 % |
2222340 |
0.62 % |
178622 |
1.34 % |
| qd2,mq40 |
70772 |
0.02 % |
60299 |
0.02 % |
10473 |
0.08 % |
| fs60 |
1804 |
0.00 % |
0 |
0.00 % |
1804 |
0.01 % |
| q20,qd2,fs60 |
1514 |
0.00 % |
0 |
0.00 % |
1514 |
0.01 % |
| qd2,fs60 |
1468 |
0.00 % |
0 |
0.00 % |
1468 |
0.01 % |
| qd2,fs60,mq40 |
1336 |
0.00 % |
0 |
0.00 % |
1336 |
0.01 % |
| fs60,mq40 |
368 |
0.00 % |
0 |
0.00 % |
368 |
0.00 % |
| q20,qd2,fs60,mq40 |
186 |
0.00 % |
0 |
0.00 % |
186 |
0.00 % |
| q20,fs60 |
4 |
0.00 % |
0 |
0.00 % |
4 |
0.00 % |
| q20,fs60,mq40 |
1 |
0.00 % |
0 |
0.00 % |
1 |
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 |
5728537 |
28.57 % |
| Transition |
G>A |
All |
1685435 |
8.41 % |
| Transition |
T>C |
All |
5543463 |
27.64 % |
| Transition |
C>T |
All |
1692064 |
8.44 % |
| Transversion |
A>C |
All |
426943 |
2.13 % |
| Transversion |
C>A |
All |
940604 |
4.69 % |
| Transversion |
T>G |
All |
440141 |
2.19 % |
| Transversion |
G>T |
All |
935928 |
4.67 % |
| Transversion |
A>T |
All |
959375 |
4.78 % |
| Transversion |
T>A |
All |
974680 |
4.86 % |
| Transversion |
C>G |
All |
367190 |
1.83 % |
| Transversion |
G>C |
All |
358117 |
1.79 % |
| |
|
|
|
|
| Transition |
A>G |
Passed |
595026 |
17.83 % |
| Transition |
G>A |
Passed |
515618 |
15.45 % |
| Transition |
T>C |
Passed |
593983 |
17.80 % |
| Transition |
C>T |
Passed |
517760 |
15.52 % |
| Transversion |
A>C |
Passed |
138331 |
4.15 % |
| Transversion |
C>A |
Passed |
150577 |
4.51 % |
| Transversion |
T>G |
Passed |
139704 |
4.19 % |
| Transversion |
G>T |
Passed |
148837 |
4.46 % |
| Transversion |
A>T |
Passed |
138390 |
4.15 % |
| Transversion |
T>A |
Passed |
138954 |
4.16 % |
| Transversion |
C>G |
Passed |
129317 |
3.88 % |
| Transversion |
G>C |
Passed |
130239 |
3.90 % |
| |
|
|
|
|
| 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 |
2.71 |
14649499 |
5402978 |
| Passed |
1.99 |
2222387 |
1114349 |
| dbSNPAll |
0 |
0 |
0 |
| dbSNPPassed |
0 |
0 |
0 |