/EXTERNAL BLUEPRINT/variants/K010471_K010472_K010473_K010474_K010475_K010476_K010477_K010478_K010479_K010480_K010481_11_lane_gembs
BACK
SAMPLE K010471_K010472_K010473_K010474_K010475_K010476_K010477_K010478_K010479_K010480_K010481_11_lane_gembs
Variant counts
| Type |
Total |
Pass |
% |
| SNPs |
944095626 |
10455964 |
1.11 % |
| Multiallelic |
0 |
0 |
0.00 % |
VCF Filtering Stats
| Type |
#Sites |
% |
#Non-Variant Sites |
% |
#Variant Sites |
% |
| All |
944095626 |
100% |
921240310 |
97.58 % |
22855316 |
2.42 % |
| |
|
|
|
|
|
|
| Passed |
20203682 |
2.14 % |
9695143 |
1.05 % |
10508539 |
52.01 % |
| Filtered |
923891944 |
97.86 % |
911545167 |
98.95 % |
12346777 |
61.11 % |
| |
|
|
|
|
|
|
| q20 |
710171341 |
76.87 % |
701642769 |
76.97 % |
8528572 |
69.08 % |
| q20,qd2 |
124227613 |
13.45 % |
121828716 |
13.37 % |
2398897 |
19.43 % |
| q20,mq40 |
63809842 |
6.91 % |
63195213 |
6.93 % |
614629 |
4.98 % |
| q20,qd2,mq40 |
24807640 |
2.69 % |
24660933 |
2.71 % |
146707 |
1.19 % |
| mq40 |
865450 |
0.09 % |
208640 |
0.02 % |
656810 |
5.32 % |
| qd2 |
7125 |
0.00 % |
6600 |
0.00 % |
525 |
0.00 % |
| qd2,mq40 |
2877 |
0.00 % |
2296 |
0.00 % |
581 |
0.00 % |
| fs60,mq40 |
20 |
0.00 % |
0 |
0.00 % |
20 |
0.00 % |
| qd2,fs60 |
17 |
0.00 % |
0 |
0.00 % |
17 |
0.00 % |
| fs60 |
10 |
0.00 % |
0 |
0.00 % |
10 |
0.00 % |
| qd2,fs60,mq40 |
4 |
0.00 % |
0 |
0.00 % |
4 |
0.00 % |
| q20,qd2,fs60,mq40 |
3 |
0.00 % |
0 |
0.00 % |
3 |
0.00 % |
| q20,qd2,fs60 |
2 |
0.00 % |
0 |
0.00 % |
2 |
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 |
6004317 |
21.95 % |
| Transition |
G>A |
All |
2177094 |
7.96 % |
| Transition |
T>C |
All |
7463837 |
27.29 % |
| Transition |
C>T |
All |
992136 |
3.63 % |
| Transversion |
A>C |
All |
946245 |
3.46 % |
| Transversion |
C>A |
All |
1861123 |
6.80 % |
| Transversion |
T>G |
All |
1163485 |
4.25 % |
| Transversion |
G>T |
All |
1650805 |
6.04 % |
| Transversion |
A>T |
All |
1323879 |
4.84 % |
| Transversion |
T>A |
All |
1822477 |
6.66 % |
| Transversion |
C>G |
All |
909889 |
3.33 % |
| Transversion |
G>C |
All |
1036107 |
3.79 % |
| |
|
|
|
|
| Transition |
A>G |
Passed |
136667 |
18.02 % |
| Transition |
G>A |
Passed |
98967 |
13.05 % |
| Transition |
T>C |
Passed |
218325 |
28.79 % |
| Transition |
C>T |
Passed |
38537 |
5.08 % |
| Transversion |
A>C |
Passed |
28912 |
3.81 % |
| Transversion |
C>A |
Passed |
45741 |
6.03 % |
| Transversion |
T>G |
Passed |
32945 |
4.34 % |
| Transversion |
G>T |
Passed |
25222 |
3.33 % |
| Transversion |
A>T |
Passed |
15690 |
2.07 % |
| Transversion |
T>A |
Passed |
43088 |
5.68 % |
| Transversion |
C>G |
Passed |
31377 |
4.14 % |
| Transversion |
G>C |
Passed |
42806 |
5.65 % |
| |
|
|
|
|
| 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 |
1.55 |
16637384 |
10714010 |
| Passed |
1.85 |
492496 |
265781 |
| dbSNPAll |
0 |
0 |
0 |
| dbSNPPassed |
0 |
0 |
0 |