/CEMT/variants/A54765_3_lane_gembs
BACK
SAMPLE A54765_3_lane_gembs
Variant counts
| Type |
Total |
Pass |
% |
| SNPs |
1170185250 |
579980631 |
49.56 % |
| Multiallelic |
0 |
0 |
0.00 % |
VCF Filtering Stats
| Type |
#Sites |
% |
#Non-Variant Sites |
% |
#Variant Sites |
% |
| All |
1170185250 |
100% |
1140901966 |
97.50 % |
29283284 |
2.50 % |
| |
|
|
|
|
|
|
| Passed |
584265327 |
49.93 % |
577837325 |
50.65 % |
6428002 |
1.10 % |
| Filtered |
585919923 |
50.07 % |
563064641 |
49.35 % |
22855282 |
3.91 % |
| |
|
|
|
|
|
|
| q20 |
518117306 |
88.43 % |
511055433 |
90.76 % |
7061873 |
30.90 % |
| q20,qd2 |
35230062 |
6.01 % |
20449307 |
3.63 % |
14780755 |
64.67 % |
| qd2 |
13731564 |
2.34 % |
13501688 |
2.40 % |
229876 |
1.01 % |
| q20,mq40 |
13048717 |
2.23 % |
12750754 |
2.26 % |
297963 |
1.30 % |
| q20,qd2,mq40 |
4004866 |
0.68 % |
3730598 |
0.66 % |
274268 |
1.20 % |
| mq40 |
1683642 |
0.29 % |
1509024 |
0.27 % |
174618 |
0.76 % |
| qd2,mq40 |
78598 |
0.01 % |
67837 |
0.01 % |
10761 |
0.05 % |
| q20,qd2,fs60 |
8875 |
0.00 % |
0 |
0.00 % |
8875 |
0.04 % |
| fs60 |
7306 |
0.00 % |
0 |
0.00 % |
7306 |
0.03 % |
| qd2,fs60 |
6616 |
0.00 % |
0 |
0.00 % |
6616 |
0.03 % |
| qd2,fs60,mq40 |
1656 |
0.00 % |
0 |
0.00 % |
1656 |
0.01 % |
| fs60,mq40 |
414 |
0.00 % |
0 |
0.00 % |
414 |
0.00 % |
| q20,qd2,fs60,mq40 |
291 |
0.00 % |
0 |
0.00 % |
291 |
0.00 % |
| q20,fs60 |
10 |
0.00 % |
0 |
0.00 % |
10 |
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 |
9437632 |
29.09 % |
| Transition |
G>A |
All |
2741347 |
8.45 % |
| Transition |
T>C |
All |
7855869 |
24.21 % |
| Transition |
C>T |
All |
2753566 |
8.49 % |
| Transversion |
A>C |
All |
769859 |
2.37 % |
| Transversion |
C>A |
All |
1663712 |
5.13 % |
| Transversion |
T>G |
All |
869936 |
2.68 % |
| Transversion |
G>T |
All |
1585848 |
4.89 % |
| Transversion |
A>T |
All |
1654345 |
5.10 % |
| Transversion |
T>A |
All |
1740390 |
5.36 % |
| Transversion |
C>G |
All |
729993 |
2.25 % |
| Transversion |
G>C |
All |
643478 |
1.98 % |
| |
|
|
|
|
| Transition |
A>G |
Passed |
570175 |
20.00 % |
| Transition |
G>A |
Passed |
406817 |
14.27 % |
| Transition |
T>C |
Passed |
524760 |
18.40 % |
| Transition |
C>T |
Passed |
409996 |
14.38 % |
| Transversion |
A>C |
Passed |
114456 |
4.01 % |
| Transversion |
C>A |
Passed |
130081 |
4.56 % |
| Transversion |
T>G |
Passed |
118296 |
4.15 % |
| Transversion |
G>T |
Passed |
128039 |
4.49 % |
| Transversion |
A>T |
Passed |
115193 |
4.04 % |
| Transversion |
T>A |
Passed |
118034 |
4.14 % |
| Transversion |
C>G |
Passed |
108460 |
3.80 % |
| Transversion |
G>C |
Passed |
106883 |
3.75 % |
| |
|
|
|
|
| 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 |
2.36 |
22788414 |
9657561 |
| Passed |
2.03 |
1911748 |
939442 |
| dbSNPAll |
0 |
0 |
0 |
| dbSNPPassed |
0 |
0 |
0 |