/cemt/variants/A75619_1_lane_gembs
BACK
SAMPLE A75619_1_lane_gembs
Variant counts
| Type |
Total |
Pass |
% |
| SNPs |
1171202357 |
967407769 |
82.60 % |
| Multiallelic |
0 |
0 |
0.00 % |
VCF Filtering Stats
| Type |
#Sites |
% |
#Non-Variant Sites |
% |
#Variant Sites |
% |
| All |
1171202357 |
100% |
1151406286 |
98.31 % |
19796071 |
1.69 % |
| |
|
|
|
|
|
|
| Passed |
970298117 |
82.85 % |
964228197 |
83.74 % |
6069920 |
0.63 % |
| Filtered |
200904240 |
17.15 % |
187178089 |
16.26 % |
13726151 |
1.41 % |
| |
|
|
|
|
|
|
| q20 |
166073687 |
82.66 % |
164849232 |
88.07 % |
1224455 |
8.92 % |
| q20,qd2 |
15533694 |
7.73 % |
4048222 |
2.16 % |
11485472 |
83.68 % |
| q20,mq40 |
11696806 |
5.82 % |
11571396 |
6.18 % |
125410 |
0.91 % |
| mq40 |
2800902 |
1.39 % |
2531183 |
1.35 % |
269719 |
1.97 % |
| q20,qd2,mq40 |
2639206 |
1.31 % |
2473195 |
1.32 % |
166011 |
1.21 % |
| qd2 |
2106702 |
1.05 % |
1662767 |
0.89 % |
443935 |
3.23 % |
| qd2,mq40 |
51613 |
0.03 % |
42094 |
0.02 % |
9519 |
0.07 % |
| qd2,fs60,mq40 |
754 |
0.00 % |
0 |
0.00 % |
754 |
0.01 % |
| qd2,fs60 |
315 |
0.00 % |
0 |
0.00 % |
315 |
0.00 % |
| fs60,mq40 |
291 |
0.00 % |
0 |
0.00 % |
291 |
0.00 % |
| fs60 |
166 |
0.00 % |
0 |
0.00 % |
166 |
0.00 % |
| q20,qd2,fs60 |
60 |
0.00 % |
0 |
0.00 % |
60 |
0.00 % |
| q20,qd2,fs60,mq40 |
44 |
0.00 % |
0 |
0.00 % |
44 |
0.00 % |
| q20,fs60 |
0 |
0.00 % |
0 |
0.00 % |
0 |
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 |
7934214 |
36.94 % |
| Transition |
G>A |
All |
968459 |
4.51 % |
| Transition |
T>C |
All |
8014181 |
37.32 % |
| Transition |
C>T |
All |
973353 |
4.53 % |
| Transversion |
A>C |
All |
385019 |
1.79 % |
| Transversion |
C>A |
All |
537807 |
2.50 % |
| Transversion |
T>G |
All |
388960 |
1.81 % |
| Transversion |
G>T |
All |
524889 |
2.44 % |
| Transversion |
A>T |
All |
504937 |
2.35 % |
| Transversion |
T>A |
All |
517649 |
2.41 % |
| Transversion |
C>G |
All |
365012 |
1.70 % |
| Transversion |
G>C |
All |
362210 |
1.69 % |
| |
|
|
|
|
| Transition |
A>G |
Passed |
930914 |
21.74 % |
| Transition |
G>A |
Passed |
583535 |
13.63 % |
| Transition |
T>C |
Passed |
838071 |
19.57 % |
| Transition |
C>T |
Passed |
582053 |
13.59 % |
| Transversion |
A>C |
Passed |
175800 |
4.11 % |
| Transversion |
C>A |
Passed |
181363 |
4.24 % |
| Transversion |
T>G |
Passed |
178362 |
4.17 % |
| Transversion |
G>T |
Passed |
171258 |
4.00 % |
| Transversion |
A>T |
Passed |
152817 |
3.57 % |
| Transversion |
T>A |
Passed |
157080 |
3.67 % |
| Transversion |
C>G |
Passed |
165965 |
3.88 % |
| Transversion |
G>C |
Passed |
164905 |
3.85 % |
| |
|
|
|
|
| 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 |
4.99 |
17890207 |
3586483 |
| Passed |
2.18 |
2934573 |
1347550 |
| dbSNPAll |
0 |
0 |
0 |
| dbSNPPassed |
0 |
0 |
0 |