/CEMT/variants/B19818_2_lane_gembs
BACK
SAMPLE B19818_2_lane_gembs
Variant counts
| Type |
Total |
Pass |
% |
| SNPs |
1165204444 |
1026371742 |
88.09 % |
| Multiallelic |
0 |
0 |
0.00 % |
VCF Filtering Stats
| Type |
#Sites |
% |
#Non-Variant Sites |
% |
#Variant Sites |
% |
| All |
1165204444 |
100% |
1150035326 |
98.70 % |
15169118 |
1.30 % |
| |
|
|
|
|
|
|
| Passed |
1027831482 |
88.21 % |
1023825993 |
89.03 % |
4005489 |
0.39 % |
| Filtered |
137372962 |
11.79 % |
126209333 |
10.97 % |
11163629 |
1.09 % |
| |
|
|
|
|
|
|
| q20 |
102971895 |
74.96 % |
101373611 |
80.32 % |
1598284 |
14.32 % |
| q20,qd2 |
14735487 |
10.73 % |
6154503 |
4.88 % |
8580984 |
76.87 % |
| q20,mq40 |
9094506 |
6.62 % |
8969067 |
7.11 % |
125439 |
1.12 % |
| mq40 |
5104103 |
3.72 % |
4816851 |
3.82 % |
287252 |
2.57 % |
| qd2 |
3211034 |
2.34 % |
2884968 |
2.29 % |
326066 |
2.92 % |
| q20,qd2,mq40 |
2105402 |
1.53 % |
1895173 |
1.50 % |
210229 |
1.88 % |
| qd2,mq40 |
136778 |
0.10 % |
115160 |
0.09 % |
21618 |
0.19 % |
| q20,qd2,fs60 |
3826 |
0.00 % |
0 |
0.00 % |
3826 |
0.03 % |
| fs60 |
3643 |
0.00 % |
0 |
0.00 % |
3643 |
0.03 % |
| qd2,fs60 |
2693 |
0.00 % |
0 |
0.00 % |
2693 |
0.02 % |
| qd2,fs60,mq40 |
2200 |
0.00 % |
0 |
0.00 % |
2200 |
0.02 % |
| fs60,mq40 |
956 |
0.00 % |
0 |
0.00 % |
956 |
0.01 % |
| q20,qd2,fs60,mq40 |
426 |
0.00 % |
0 |
0.00 % |
426 |
0.00 % |
| q20,fs60,mq40 |
9 |
0.00 % |
0 |
0.00 % |
9 |
0.00 % |
| q20,fs60 |
4 |
0.00 % |
0 |
0.00 % |
4 |
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 |
4379648 |
22.93 % |
| Transition |
G>A |
All |
3996455 |
20.92 % |
| Transition |
T>C |
All |
4290197 |
22.46 % |
| Transition |
C>T |
All |
4010273 |
20.99 % |
| Transversion |
A>C |
All |
289437 |
1.52 % |
| Transversion |
C>A |
All |
354386 |
1.86 % |
| Transversion |
T>G |
All |
299850 |
1.57 % |
| Transversion |
G>T |
All |
352299 |
1.84 % |
| Transversion |
A>T |
All |
319435 |
1.67 % |
| Transversion |
T>A |
All |
321186 |
1.68 % |
| Transversion |
C>G |
All |
248621 |
1.30 % |
| Transversion |
G>C |
All |
241381 |
1.26 % |
| |
|
|
|
|
| Transition |
A>G |
Passed |
681580 |
18.28 % |
| Transition |
G>A |
Passed |
588660 |
15.79 % |
| Transition |
T>C |
Passed |
685585 |
18.39 % |
| Transition |
C>T |
Passed |
589655 |
15.81 % |
| Transversion |
A>C |
Passed |
157731 |
4.23 % |
| Transversion |
C>A |
Passed |
155231 |
4.16 % |
| Transversion |
T>G |
Passed |
158070 |
4.24 % |
| Transversion |
G>T |
Passed |
148511 |
3.98 % |
| Transversion |
A>T |
Passed |
122516 |
3.29 % |
| Transversion |
T>A |
Passed |
123632 |
3.32 % |
| Transversion |
C>G |
Passed |
158854 |
4.26 % |
| Transversion |
G>C |
Passed |
158787 |
4.26 % |
| |
|
|
|
|
| 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 |
6.87 |
16676573 |
2426595 |
| Passed |
2.15 |
2545480 |
1183332 |
| dbSNPAll |
0 |
0 |
0 |
| dbSNPPassed |
0 |
0 |
0 |