/EXTERNAL BLUEPRINT/variants/K012038_K012079_K012116_K012117_4_lane_gembs
BACK
SAMPLE K012038_K012079_K012116_K012117_4_lane_gembs
Variant counts
| Type |
Total |
Pass |
% |
| SNPs |
889189618 |
5069385 |
0.57 % |
| Multiallelic |
0 |
0 |
0.00 % |
VCF Filtering Stats
| Type |
#Sites |
% |
#Non-Variant Sites |
% |
#Variant Sites |
% |
| All |
889189618 |
100% |
872435644 |
98.12 % |
16753974 |
1.88 % |
| |
|
|
|
|
|
|
| Passed |
14156937 |
1.59 % |
4659277 |
0.53 % |
9497660 |
67.09 % |
| Filtered |
875032681 |
98.41 % |
867776367 |
99.47 % |
7256314 |
51.26 % |
| |
|
|
|
|
|
|
| q20 |
675177190 |
77.16 % |
670037531 |
77.21 % |
5139659 |
70.83 % |
| q20,qd2 |
126138960 |
14.42 % |
124877135 |
14.39 % |
1261825 |
17.39 % |
| q20,mq40 |
52148542 |
5.96 % |
51843377 |
5.97 % |
305165 |
4.21 % |
| q20,qd2,mq40 |
20983876 |
2.40 % |
20911903 |
2.41 % |
71973 |
0.99 % |
| mq40 |
574984 |
0.07 % |
97926 |
0.01 % |
477058 |
6.57 % |
| qd2 |
7271 |
0.00 % |
7003 |
0.00 % |
268 |
0.00 % |
| qd2,mq40 |
1821 |
0.00 % |
1492 |
0.00 % |
329 |
0.00 % |
| fs60,mq40 |
12 |
0.00 % |
0 |
0.00 % |
12 |
0.00 % |
| qd2,fs60 |
9 |
0.00 % |
0 |
0.00 % |
9 |
0.00 % |
| fs60 |
8 |
0.00 % |
0 |
0.00 % |
8 |
0.00 % |
| 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,qd2,fs60,mq40 |
2 |
0.00 % |
0 |
0.00 % |
2 |
0.00 % |
| q20,fs60,mq40 |
1 |
0.00 % |
0 |
0.00 % |
1 |
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 |
4982794 |
23.51 % |
| Transition |
G>A |
All |
1705196 |
8.05 % |
| Transition |
T>C |
All |
6108101 |
28.82 % |
| Transition |
C>T |
All |
786421 |
3.71 % |
| Transversion |
A>C |
All |
655214 |
3.09 % |
| Transversion |
C>A |
All |
1304062 |
6.15 % |
| Transversion |
T>G |
All |
844526 |
3.99 % |
| Transversion |
G>T |
All |
1159858 |
5.47 % |
| Transversion |
A>T |
All |
914568 |
4.32 % |
| Transversion |
T>A |
All |
1314770 |
6.20 % |
| Transversion |
C>G |
All |
659241 |
3.11 % |
| Transversion |
G>C |
All |
756142 |
3.57 % |
| |
|
|
|
|
| Transition |
A>G |
Passed |
71332 |
17.53 % |
| Transition |
G>A |
Passed |
56045 |
13.77 % |
| Transition |
T>C |
Passed |
106810 |
26.24 % |
| Transition |
C>T |
Passed |
25148 |
6.18 % |
| Transversion |
A>C |
Passed |
16634 |
4.09 % |
| Transversion |
C>A |
Passed |
24042 |
5.91 % |
| Transversion |
T>G |
Passed |
18928 |
4.65 % |
| Transversion |
G>T |
Passed |
13578 |
3.34 % |
| Transversion |
A>T |
Passed |
8534 |
2.10 % |
| Transversion |
T>A |
Passed |
22404 |
5.50 % |
| Transversion |
C>G |
Passed |
18957 |
4.66 % |
| Transversion |
G>C |
Passed |
24579 |
6.04 % |
| |
|
|
|
|
| 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 |
1.79 |
13582512 |
7608381 |
| Passed |
1.76 |
259335 |
147656 |
| dbSNPAll |
0 |
0 |
0 |
| dbSNPPassed |
0 |
0 |
0 |