/CEMT/variants/B35055_1_lane_gembs
BACK
SAMPLE B35055_1_lane_gembs
Variant counts
| Type |
Total |
Pass |
% |
| SNPs |
1168830053 |
1030310739 |
88.15 % |
| Multiallelic |
0 |
0 |
0.00 % |
VCF Filtering Stats
| Type |
#Sites |
% |
#Non-Variant Sites |
% |
#Variant Sites |
% |
| All |
1168830053 |
100% |
1152270578 |
98.58 % |
16559475 |
1.42 % |
| |
|
|
|
|
|
|
| Passed |
1032321420 |
88.32 % |
1027229211 |
89.15 % |
5092209 |
0.49 % |
| Filtered |
136508633 |
11.68 % |
125041367 |
10.85 % |
11467266 |
1.11 % |
| |
|
|
|
|
|
|
| q20 |
107113814 |
78.47 % |
106305790 |
85.02 % |
808024 |
7.05 % |
| q20,qd2 |
13048096 |
9.56 % |
3233840 |
2.59 % |
9814256 |
85.58 % |
| q20,mq40 |
9624092 |
7.05 % |
9525420 |
7.62 % |
98672 |
0.86 % |
| q20,qd2,mq40 |
2447746 |
1.79 % |
2310694 |
1.85 % |
137052 |
1.20 % |
| mq40 |
2273293 |
1.67 % |
2036093 |
1.63 % |
237200 |
2.07 % |
| qd2 |
1948418 |
1.43 % |
1588140 |
1.27 % |
360278 |
3.14 % |
| qd2,mq40 |
51178 |
0.04 % |
41390 |
0.03 % |
9788 |
0.09 % |
| qd2,fs60,mq40 |
833 |
0.00 % |
0 |
0.00 % |
833 |
0.01 % |
| qd2,fs60 |
446 |
0.00 % |
0 |
0.00 % |
446 |
0.00 % |
| fs60,mq40 |
289 |
0.00 % |
0 |
0.00 % |
289 |
0.00 % |
| fs60 |
250 |
0.00 % |
0 |
0.00 % |
250 |
0.00 % |
| q20,qd2,fs60 |
95 |
0.00 % |
0 |
0.00 % |
95 |
0.00 % |
| q20,qd2,fs60,mq40 |
79 |
0.00 % |
0 |
0.00 % |
79 |
0.00 % |
| q20,fs60 |
2 |
0.00 % |
0 |
0.00 % |
2 |
0.00 % |
| q20,fs60,mq40 |
2 |
0.00 % |
0 |
0.00 % |
2 |
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 |
6699098 |
36.73 % |
| Transition |
G>A |
All |
971300 |
5.33 % |
| Transition |
T>C |
All |
6664414 |
36.54 % |
| Transition |
C>T |
All |
973465 |
5.34 % |
| Transversion |
A>C |
All |
339275 |
1.86 % |
| Transversion |
C>A |
All |
429987 |
2.36 % |
| Transversion |
T>G |
All |
343499 |
1.88 % |
| Transversion |
G>T |
All |
424654 |
2.33 % |
| Transversion |
A>T |
All |
396383 |
2.17 % |
| Transversion |
T>A |
All |
400145 |
2.19 % |
| Transversion |
C>G |
All |
300381 |
1.65 % |
| Transversion |
G>C |
All |
297122 |
1.63 % |
| |
|
|
|
|
| Transition |
A>G |
Passed |
804967 |
18.80 % |
| Transition |
G>A |
Passed |
631364 |
14.75 % |
| Transition |
T>C |
Passed |
806081 |
18.83 % |
| Transition |
C>T |
Passed |
632028 |
14.76 % |
| Transversion |
A>C |
Passed |
186178 |
4.35 % |
| Transversion |
C>A |
Passed |
188745 |
4.41 % |
| Transversion |
T>G |
Passed |
186031 |
4.34 % |
| Transversion |
G>T |
Passed |
181255 |
4.23 % |
| Transversion |
A>T |
Passed |
158384 |
3.70 % |
| Transversion |
T>A |
Passed |
161630 |
3.77 % |
| Transversion |
C>G |
Passed |
172198 |
4.02 % |
| Transversion |
G>C |
Passed |
172801 |
4.04 % |
| |
|
|
|
|
| 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 |
5.22 |
15308277 |
2931446 |
| Passed |
2.04 |
2874440 |
1407222 |
| dbSNPAll |
0 |
0 |
0 |
| dbSNPPassed |
0 |
0 |
0 |