/cemt/variants/A36017_3_lane_gembs
BACK
SAMPLE A36017_3_lane_gembs
Variant counts
| Type |
Total |
Pass |
% |
| SNPs |
1165611291 |
737033937 |
63.23 % |
| Multiallelic |
0 |
0 |
0.00 % |
VCF Filtering Stats
| Type |
#Sites |
% |
#Non-Variant Sites |
% |
#Variant Sites |
% |
| All |
1165611291 |
100% |
1145518703 |
98.28 % |
20092588 |
1.72 % |
| |
|
|
|
|
|
|
| Passed |
739809464 |
63.47 % |
734692341 |
64.14 % |
5117123 |
0.69 % |
| Filtered |
425801827 |
36.53 % |
410826362 |
35.86 % |
14975465 |
2.02 % |
| |
|
|
|
|
|
|
| q20 |
377415411 |
88.64 % |
373817984 |
90.99 % |
3597427 |
24.02 % |
| q20,qd2 |
24236968 |
5.69 % |
13696653 |
3.33 % |
10540315 |
70.38 % |
| q20,mq40 |
11375434 |
2.67 % |
11166434 |
2.72 % |
209000 |
1.40 % |
| qd2 |
7482460 |
1.76 % |
7273755 |
1.77 % |
208705 |
1.39 % |
| q20,qd2,mq40 |
3371069 |
0.79 % |
3140299 |
0.76 % |
230770 |
1.54 % |
| mq40 |
1837724 |
0.43 % |
1672887 |
0.41 % |
164837 |
1.10 % |
| qd2,mq40 |
68651 |
0.02 % |
58350 |
0.01 % |
10301 |
0.07 % |
| fs60 |
4663 |
0.00 % |
0 |
0.00 % |
4663 |
0.03 % |
| q20,qd2,fs60 |
4048 |
0.00 % |
0 |
0.00 % |
4048 |
0.03 % |
| qd2,fs60 |
3284 |
0.00 % |
0 |
0.00 % |
3284 |
0.02 % |
| qd2,fs60,mq40 |
1512 |
0.00 % |
0 |
0.00 % |
1512 |
0.01 % |
| fs60,mq40 |
380 |
0.00 % |
0 |
0.00 % |
380 |
0.00 % |
| q20,qd2,fs60,mq40 |
211 |
0.00 % |
0 |
0.00 % |
211 |
0.00 % |
| q20,fs60 |
11 |
0.00 % |
0 |
0.00 % |
11 |
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 |
6096424 |
27.24 % |
| Transition |
G>A |
All |
2028455 |
9.06 % |
| Transition |
T>C |
All |
5946951 |
26.57 % |
| Transition |
C>T |
All |
2018517 |
9.02 % |
| Transversion |
A>C |
All |
405916 |
1.81 % |
| Transversion |
C>A |
All |
1271870 |
5.68 % |
| Transversion |
T>G |
All |
412110 |
1.84 % |
| Transversion |
G>T |
All |
1274641 |
5.70 % |
| Transversion |
A>T |
All |
1129290 |
5.05 % |
| Transversion |
T>A |
All |
1135065 |
5.07 % |
| Transversion |
C>G |
All |
334474 |
1.49 % |
| Transversion |
G>C |
All |
326186 |
1.46 % |
| |
|
|
|
|
| Transition |
A>G |
Passed |
564995 |
17.43 % |
| Transition |
G>A |
Passed |
513136 |
15.83 % |
| Transition |
T>C |
Passed |
566887 |
17.48 % |
| Transition |
C>T |
Passed |
515802 |
15.91 % |
| Transversion |
A>C |
Passed |
131135 |
4.04 % |
| Transversion |
C>A |
Passed |
150309 |
4.64 % |
| Transversion |
T>G |
Passed |
131197 |
4.05 % |
| Transversion |
G>T |
Passed |
148119 |
4.57 % |
| Transversion |
A>T |
Passed |
135870 |
4.19 % |
| Transversion |
T>A |
Passed |
137538 |
4.24 % |
| Transversion |
C>G |
Passed |
123639 |
3.81 % |
| Transversion |
G>C |
Passed |
123673 |
3.81 % |
| |
|
|
|
|
| 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 |
2.56 |
16090347 |
6289552 |
| Passed |
2.00 |
2160820 |
1081480 |
| dbSNPAll |
0 |
0 |
0 |
| dbSNPPassed |
0 |
0 |
0 |