/CEMT/variants/A91239_2_lane_gembs
BACK
SAMPLE A91239_2_lane_gembs
Variant counts
| Type |
Total |
Pass |
% |
| SNPs |
1165746101 |
1048303549 |
89.93 % |
| Multiallelic |
0 |
0 |
0.00 % |
VCF Filtering Stats
| Type |
#Sites |
% |
#Non-Variant Sites |
% |
#Variant Sites |
% |
| All |
1165746101 |
100% |
1153718634 |
98.97 % |
12027467 |
1.03 % |
| |
|
|
|
|
|
|
| Passed |
1049594966 |
90.04 % |
1045580934 |
90.63 % |
4014032 |
0.38 % |
| Filtered |
116151135 |
9.96 % |
108137700 |
9.37 % |
8013435 |
0.76 % |
| |
|
|
|
|
|
|
| q20 |
87336953 |
75.19 % |
86460252 |
79.95 % |
876701 |
10.94 % |
| q20,mq40 |
10668789 |
9.19 % |
10519611 |
9.73 % |
149178 |
1.86 % |
| q20,qd2 |
8908403 |
7.67 % |
2723430 |
2.52 % |
6184973 |
77.18 % |
| mq40 |
3831599 |
3.30 % |
3529087 |
3.26 % |
302512 |
3.78 % |
| qd2 |
2770452 |
2.39 % |
2494163 |
2.31 % |
276289 |
3.45 % |
| q20,qd2,mq40 |
2547709 |
2.19 % |
2343054 |
2.17 % |
204655 |
2.55 % |
| qd2,mq40 |
82661 |
0.07 % |
68103 |
0.06 % |
14558 |
0.18 % |
| qd2,fs60,mq40 |
1650 |
0.00 % |
0 |
0.00 % |
1650 |
0.02 % |
| qd2,fs60 |
1026 |
0.00 % |
0 |
0.00 % |
1026 |
0.01 % |
| fs60 |
976 |
0.00 % |
0 |
0.00 % |
976 |
0.01 % |
| fs60,mq40 |
482 |
0.00 % |
0 |
0.00 % |
482 |
0.01 % |
| q20,qd2,fs60 |
303 |
0.00 % |
0 |
0.00 % |
303 |
0.00 % |
| q20,qd2,fs60,mq40 |
129 |
0.00 % |
0 |
0.00 % |
129 |
0.00 % |
| q20,fs60 |
2 |
0.00 % |
0 |
0.00 % |
2 |
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 |
4600055 |
33.04 % |
| Transition |
G>A |
All |
944689 |
6.79 % |
| Transition |
T>C |
All |
4592820 |
32.99 % |
| Transition |
C>T |
All |
944824 |
6.79 % |
| Transversion |
A>C |
All |
348410 |
2.50 % |
| Transversion |
C>A |
All |
393211 |
2.82 % |
| Transversion |
T>G |
All |
353292 |
2.54 % |
| Transversion |
G>T |
All |
388418 |
2.79 % |
| Transversion |
A>T |
All |
365857 |
2.63 % |
| Transversion |
T>A |
All |
370098 |
2.66 % |
| Transversion |
C>G |
All |
310907 |
2.23 % |
| Transversion |
G>C |
All |
310296 |
2.23 % |
| |
|
|
|
|
| Transition |
A>G |
Passed |
741757 |
18.06 % |
| Transition |
G>A |
Passed |
621068 |
15.12 % |
| Transition |
T>C |
Passed |
745172 |
18.14 % |
| Transition |
C>T |
Passed |
620358 |
15.10 % |
| Transversion |
A>C |
Passed |
184360 |
4.49 % |
| Transversion |
C>A |
Passed |
182520 |
4.44 % |
| Transversion |
T>G |
Passed |
183978 |
4.48 % |
| Transversion |
G>T |
Passed |
174776 |
4.26 % |
| Transversion |
A>T |
Passed |
155666 |
3.79 % |
| Transversion |
T>A |
Passed |
157927 |
3.84 % |
| Transversion |
C>G |
Passed |
169809 |
4.13 % |
| Transversion |
G>C |
Passed |
170122 |
4.14 % |
| |
|
|
|
|
| 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 |
3.90 |
11082388 |
2840489 |
| Passed |
1.98 |
2728355 |
1379158 |
| dbSNPAll |
0 |
0 |
0 |
| dbSNPPassed |
0 |
0 |
0 |