/cemt/variants/A36015_3_lane_gembs
BACK
SAMPLE A36015_3_lane_gembs
Variant counts
| Type |
Total |
Pass |
% |
| SNPs |
1154295570 |
631069833 |
54.67 % |
| Multiallelic |
0 |
0 |
0.00 % |
VCF Filtering Stats
| Type |
#Sites |
% |
#Non-Variant Sites |
% |
#Variant Sites |
% |
| All |
1154295570 |
100% |
1134789329 |
98.31 % |
19506241 |
1.69 % |
| |
|
|
|
|
|
|
| Passed |
634089626 |
54.93 % |
629054969 |
55.43 % |
5034657 |
0.79 % |
| Filtered |
520205944 |
45.07 % |
505734360 |
44.57 % |
14471584 |
2.28 % |
| |
|
|
|
|
|
|
| q20 |
470092429 |
90.37 % |
466099426 |
92.16 % |
3993003 |
27.59 % |
| q20,qd2 |
28994293 |
5.57 % |
19223371 |
3.80 % |
9770922 |
67.52 % |
| q20,mq40 |
10841193 |
2.08 % |
10664941 |
2.11 % |
176252 |
1.22 % |
| qd2 |
5187773 |
1.00 % |
5006597 |
0.99 % |
181176 |
1.25 % |
| q20,qd2,mq40 |
3388282 |
0.65 % |
3203430 |
0.63 % |
184852 |
1.28 % |
| mq40 |
1639625 |
0.32 % |
1491771 |
0.29 % |
147854 |
1.02 % |
| qd2,mq40 |
53478 |
0.01 % |
44824 |
0.01 % |
8654 |
0.06 % |
| q20,qd2,fs60 |
2738 |
0.00 % |
0 |
0.00 % |
2738 |
0.02 % |
| fs60 |
2497 |
0.00 % |
0 |
0.00 % |
2497 |
0.02 % |
| qd2,fs60 |
1944 |
0.00 % |
0 |
0.00 % |
1944 |
0.01 % |
| qd2,fs60,mq40 |
1222 |
0.00 % |
0 |
0.00 % |
1222 |
0.01 % |
| fs60,mq40 |
292 |
0.00 % |
0 |
0.00 % |
292 |
0.00 % |
| q20,qd2,fs60,mq40 |
172 |
0.00 % |
0 |
0.00 % |
172 |
0.00 % |
| q20,fs60 |
6 |
0.00 % |
0 |
0.00 % |
6 |
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 |
5777706 |
26.22 % |
| Transition |
G>A |
All |
2113999 |
9.59 % |
| Transition |
T>C |
All |
5473329 |
24.84 % |
| Transition |
C>T |
All |
2122820 |
9.63 % |
| Transversion |
A>C |
All |
451148 |
2.05 % |
| Transversion |
C>A |
All |
1348163 |
6.12 % |
| Transversion |
T>G |
All |
461735 |
2.10 % |
| Transversion |
G>T |
All |
1335681 |
6.06 % |
| Transversion |
A>T |
All |
1103401 |
5.01 % |
| Transversion |
T>A |
All |
1120650 |
5.09 % |
| Transversion |
C>G |
All |
367570 |
1.67 % |
| Transversion |
G>C |
All |
358097 |
1.63 % |
| |
|
|
|
|
| Transition |
A>G |
Passed |
488059 |
17.53 % |
| Transition |
G>A |
Passed |
441318 |
15.85 % |
| Transition |
T>C |
Passed |
483839 |
17.38 % |
| Transition |
C>T |
Passed |
443498 |
15.93 % |
| Transversion |
A>C |
Passed |
113139 |
4.06 % |
| Transversion |
C>A |
Passed |
127379 |
4.58 % |
| Transversion |
T>G |
Passed |
113501 |
4.08 % |
| Transversion |
G>T |
Passed |
125194 |
4.50 % |
| Transversion |
A>T |
Passed |
116528 |
4.19 % |
| Transversion |
T>A |
Passed |
118765 |
4.27 % |
| Transversion |
C>G |
Passed |
106201 |
3.81 % |
| Transversion |
G>C |
Passed |
106768 |
3.83 % |
| |
|
|
|
|
| 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 |
2.37 |
15487854 |
6546445 |
| Passed |
2.00 |
1856714 |
927475 |
| dbSNPAll |
0 |
0 |
0 |
| dbSNPPassed |
0 |
0 |
0 |