/cemt/variants/A34003_3_lane_gembs
BACK
SAMPLE A34003_3_lane_gembs
Variant counts
| Type |
Total |
Pass |
% |
| SNPs |
1155061934 |
853331244 |
73.88 % |
| Multiallelic |
0 |
0 |
0.00 % |
VCF Filtering Stats
| Type |
#Sites |
% |
#Non-Variant Sites |
% |
#Variant Sites |
% |
| All |
1155061934 |
100% |
1136345686 |
98.38 % |
18716248 |
1.62 % |
| |
|
|
|
|
|
|
| Passed |
856196779 |
74.13 % |
850882167 |
74.88 % |
5314612 |
0.62 % |
| Filtered |
298865155 |
25.87 % |
285463519 |
25.12 % |
13401636 |
1.57 % |
| |
|
|
|
|
|
|
| q20 |
259251340 |
86.75 % |
257770271 |
90.30 % |
1481069 |
11.05 % |
| q20,mq40 |
16422659 |
5.50 % |
16324809 |
5.72 % |
97850 |
0.73 % |
| q20,qd2 |
15579497 |
5.21 % |
4291933 |
1.50 % |
11287564 |
84.23 % |
| mq40 |
3756794 |
1.26 % |
3526951 |
1.24 % |
229843 |
1.72 % |
| q20,qd2,mq40 |
2987046 |
1.00 % |
2834093 |
0.99 % |
152953 |
1.14 % |
| qd2 |
829591 |
0.28 % |
685443 |
0.24 % |
144148 |
1.08 % |
| qd2,mq40 |
37173 |
0.01 % |
30019 |
0.01 % |
7154 |
0.05 % |
| qd2,fs60,mq40 |
457 |
0.00 % |
0 |
0.00 % |
457 |
0.00 % |
| fs60,mq40 |
246 |
0.00 % |
0 |
0.00 % |
246 |
0.00 % |
| qd2,fs60 |
196 |
0.00 % |
0 |
0.00 % |
196 |
0.00 % |
| q20,qd2,fs60,mq40 |
72 |
0.00 % |
0 |
0.00 % |
72 |
0.00 % |
| fs60 |
57 |
0.00 % |
0 |
0.00 % |
57 |
0.00 % |
| q20,qd2,fs60 |
25 |
0.00 % |
0 |
0.00 % |
25 |
0.00 % |
| q20,fs60,mq40 |
2 |
0.00 % |
0 |
0.00 % |
2 |
0.00 % |
| q20,fs60 |
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 |
8060219 |
39.68 % |
| Transition |
G>A |
All |
976344 |
4.81 % |
| Transition |
T>C |
All |
7765917 |
38.23 % |
| Transition |
C>T |
All |
982948 |
4.84 % |
| Transversion |
A>C |
All |
202954 |
1.00 % |
| Transversion |
C>A |
All |
466631 |
2.30 % |
| Transversion |
T>G |
All |
211080 |
1.04 % |
| Transversion |
G>T |
All |
453791 |
2.23 % |
| Transversion |
A>T |
All |
387581 |
1.91 % |
| Transversion |
T>A |
All |
394303 |
1.94 % |
| Transversion |
C>G |
All |
207915 |
1.02 % |
| Transversion |
G>C |
All |
204032 |
1.00 % |
| |
|
|
|
|
| Transition |
A>G |
Passed |
618313 |
18.28 % |
| Transition |
G>A |
Passed |
524373 |
15.50 % |
| Transition |
T>C |
Passed |
614081 |
18.16 % |
| Transition |
C>T |
Passed |
528339 |
15.62 % |
| Transversion |
A>C |
Passed |
136726 |
4.04 % |
| Transversion |
C>A |
Passed |
145367 |
4.30 % |
| Transversion |
T>G |
Passed |
137190 |
4.06 % |
| Transversion |
G>T |
Passed |
145326 |
4.30 % |
| Transversion |
A>T |
Passed |
129127 |
3.82 % |
| Transversion |
T>A |
Passed |
130194 |
3.85 % |
| Transversion |
C>G |
Passed |
136087 |
4.02 % |
| Transversion |
G>C |
Passed |
137026 |
4.05 % |
| |
|
|
|
|
| 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 |
7.03 |
17785428 |
2528287 |
| Passed |
2.08 |
2285106 |
1097043 |
| dbSNPAll |
0 |
0 |
0 |
| dbSNPPassed |
0 |
0 |
0 |