/cemt/variants/K005744_0_lane_gembs
BACK
SAMPLE K005744_0_lane_gembs
Variant counts
| Type |
Total |
Pass |
% |
| SNPs |
1171958329 |
890715038 |
76.00 % |
| Multiallelic |
0 |
0 |
0.00 % |
VCF Filtering Stats
| Type |
#Sites |
% |
#Non-Variant Sites |
% |
#Variant Sites |
% |
| All |
1171958329 |
100% |
1156883512 |
98.71 % |
15074817 |
1.29 % |
| |
|
|
|
|
|
|
| Passed |
893590155 |
76.25 % |
888082105 |
76.77 % |
5508050 |
0.62 % |
| Filtered |
278368174 |
23.75 % |
268801407 |
23.23 % |
9566767 |
1.07 % |
| |
|
|
|
|
|
|
| q20 |
248234341 |
89.17 % |
246520043 |
91.71 % |
1714298 |
17.92 % |
| q20,qd2 |
12037013 |
4.32 % |
5039972 |
1.87 % |
6997041 |
73.14 % |
| q20,mq40 |
10031611 |
3.60 % |
9902189 |
3.68 % |
129422 |
1.35 % |
| mq40 |
3126377 |
1.12 % |
2857794 |
1.06 % |
268583 |
2.81 % |
| q20,qd2,mq40 |
2549548 |
0.92 % |
2378199 |
0.88 % |
171349 |
1.79 % |
| qd2 |
2317256 |
0.83 % |
2046992 |
0.76 % |
270264 |
2.83 % |
| qd2,mq40 |
68988 |
0.02 % |
56218 |
0.02 % |
12770 |
0.13 % |
| qd2,fs60,mq40 |
1177 |
0.00 % |
0 |
0.00 % |
1177 |
0.01 % |
| qd2,fs60 |
805 |
0.00 % |
0 |
0.00 % |
805 |
0.01 % |
| fs60 |
524 |
0.00 % |
0 |
0.00 % |
524 |
0.01 % |
| fs60,mq40 |
297 |
0.00 % |
0 |
0.00 % |
297 |
0.00 % |
| q20,qd2,fs60 |
143 |
0.00 % |
0 |
0.00 % |
143 |
0.00 % |
| q20,qd2,fs60,mq40 |
91 |
0.00 % |
0 |
0.00 % |
91 |
0.00 % |
| q20,fs60,mq40 |
3 |
0.00 % |
0 |
0.00 % |
3 |
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 |
6079676 |
35.96 % |
| Transition |
G>A |
All |
969197 |
5.73 % |
| Transition |
T>C |
All |
5532619 |
32.73 % |
| Transition |
C>T |
All |
1032507 |
6.11 % |
| Transversion |
A>C |
All |
346800 |
2.05 % |
| Transversion |
C>A |
All |
527392 |
3.12 % |
| Transversion |
T>G |
All |
372837 |
2.21 % |
| Transversion |
G>T |
All |
509948 |
3.02 % |
| Transversion |
A>T |
All |
385304 |
2.28 % |
| Transversion |
T>A |
All |
405339 |
2.40 % |
| Transversion |
C>G |
All |
382538 |
2.26 % |
| Transversion |
G>C |
All |
361184 |
2.14 % |
| |
|
|
|
|
| Transition |
A>G |
Passed |
705665 |
18.97 % |
| Transition |
G>A |
Passed |
551632 |
14.83 % |
| Transition |
T>C |
Passed |
680256 |
18.28 % |
| Transition |
C>T |
Passed |
556997 |
14.97 % |
| Transversion |
A>C |
Passed |
154917 |
4.16 % |
| Transversion |
C>A |
Passed |
162010 |
4.35 % |
| Transversion |
T>G |
Passed |
156055 |
4.19 % |
| Transversion |
G>T |
Passed |
157972 |
4.25 % |
| Transversion |
A>T |
Passed |
145931 |
3.92 % |
| Transversion |
T>A |
Passed |
146855 |
3.95 % |
| Transversion |
C>G |
Passed |
151125 |
4.06 % |
| Transversion |
G>C |
Passed |
150960 |
4.06 % |
| |
|
|
|
|
| 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 |
4.14 |
13613999 |
3291342 |
| Passed |
2.03 |
2494550 |
1225825 |
| dbSNPAll |
0 |
0 |
0 |
| dbSNPPassed |
0 |
0 |
0 |