/EXTERNAL BLUEPRINT/variants/K012132_1_lane_gembs
BACK
SAMPLE K012132_1_lane_gembs
Variant counts
| Type |
Total |
Pass |
% |
| SNPs |
509736868 |
64208 |
0.01 % |
| Multiallelic |
0 |
0 |
0.00 % |
VCF Filtering Stats
| Type |
#Sites |
% |
#Non-Variant Sites |
% |
#Variant Sites |
% |
| All |
509736868 |
100% |
505627845 |
99.19 % |
4109023 |
0.81 % |
| |
|
|
|
|
|
|
| Passed |
1804170 |
0.35 % |
37625 |
0.01 % |
1766545 |
97.91 % |
| Filtered |
507932698 |
99.65 % |
505590220 |
99.99 % |
2342478 |
129.84 % |
| |
|
|
|
|
|
|
| q20 |
302137931 |
59.48 % |
300227416 |
59.38 % |
1910515 |
81.56 % |
| q20,qd2 |
149902147 |
29.51 % |
149772579 |
29.62 % |
129568 |
5.53 % |
| q20,mq40 |
33985009 |
6.69 % |
33824122 |
6.69 % |
160887 |
6.87 % |
| q20,qd2,mq40 |
21766719 |
4.29 % |
21751985 |
4.30 % |
14734 |
0.63 % |
| mq40 |
139031 |
0.03 % |
12358 |
0.00 % |
126673 |
5.41 % |
| qd2 |
1555 |
0.00 % |
1520 |
0.00 % |
35 |
0.00 % |
| qd2,mq40 |
293 |
0.00 % |
240 |
0.00 % |
53 |
0.00 % |
| fs60 |
8 |
0.00 % |
0 |
0.00 % |
8 |
0.00 % |
| qd2,fs60 |
4 |
0.00 % |
0 |
0.00 % |
4 |
0.00 % |
| q20,qd2,fs60 |
1 |
0.00 % |
0 |
0.00 % |
1 |
0.00 % |
| q20,fs60 |
0 |
0.00 % |
0 |
0.00 % |
0 |
0.00 % |
| fs60,mq40 |
0 |
0.00 % |
0 |
0.00 % |
0 |
0.00 % |
| q20,fs60,mq40 |
0 |
0.00 % |
0 |
0.00 % |
0 |
0.00 % |
| qd2,fs60,mq40 |
0 |
0.00 % |
0 |
0.00 % |
0 |
0.00 % |
| q20,qd2,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 |
2059412 |
23.46 % |
| Transition |
G>A |
All |
598228 |
6.81 % |
| Transition |
T>C |
All |
2591697 |
29.52 % |
| Transition |
C>T |
All |
298067 |
3.40 % |
| Transversion |
A>C |
All |
452621 |
5.16 % |
| Transversion |
C>A |
All |
423917 |
4.83 % |
| Transversion |
T>G |
All |
552545 |
6.29 % |
| Transversion |
G>T |
All |
382233 |
4.35 % |
| Transversion |
A>T |
All |
306557 |
3.49 % |
| Transversion |
T>A |
All |
436481 |
4.97 % |
| Transversion |
C>G |
All |
327443 |
3.73 % |
| Transversion |
G>C |
All |
350253 |
3.99 % |
| |
|
|
|
|
| Transition |
A>G |
Passed |
3866 |
14.83 % |
| Transition |
G>A |
Passed |
2945 |
11.29 % |
| Transition |
T>C |
Passed |
6872 |
26.35 % |
| Transition |
C>T |
Passed |
1907 |
7.31 % |
| Transversion |
A>C |
Passed |
1095 |
4.20 % |
| Transversion |
C>A |
Passed |
1510 |
5.79 % |
| Transversion |
T>G |
Passed |
1381 |
5.30 % |
| Transversion |
G>T |
Passed |
1429 |
5.48 % |
| Transversion |
A>T |
Passed |
750 |
2.88 % |
| Transversion |
T>A |
Passed |
1139 |
4.37 % |
| Transversion |
C>G |
Passed |
1474 |
5.65 % |
| Transversion |
G>C |
Passed |
1709 |
6.55 % |
| |
|
|
|
|
| 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 |
1.72 |
5547404 |
3232050 |
| Passed |
1.49 |
15590 |
10487 |
| dbSNPAll |
0 |
0 |
0 |
| dbSNPPassed |
0 |
0 |
0 |