/EXTERNAL KNIH/variants/K006243_1_lane_gembs
BACK
SAMPLE K006243_1_lane_gembs
Variant counts
| Type |
Total |
Pass |
% |
| SNPs |
1193943517 |
713213298 |
59.74 % |
| Multiallelic |
0 |
0 |
0.00 % |
VCF Filtering Stats
| Type |
#Sites |
% |
#Non-Variant Sites |
% |
#Variant Sites |
% |
| All |
1193943517 |
100% |
1134774672 |
95.04 % |
59168845 |
4.96 % |
| |
|
|
|
|
|
|
| Passed |
724687763 |
60.70 % |
703752190 |
62.02 % |
20935573 |
2.89 % |
| Filtered |
469255754 |
39.30 % |
431022482 |
37.98 % |
38233272 |
5.28 % |
| |
|
|
|
|
|
|
| q20 |
405603991 |
86.44 % |
392923906 |
91.16 % |
12680085 |
33.17 % |
| q20,qd2 |
46838633 |
9.98 % |
23284236 |
5.40 % |
23554397 |
61.61 % |
| qd2 |
9446181 |
2.01 % |
7780723 |
1.81 % |
1665458 |
4.36 % |
| q20,mq40 |
4765953 |
1.02 % |
4651471 |
1.08 % |
114482 |
0.30 % |
| q20,qd2,mq40 |
2033041 |
0.43 % |
1960803 |
0.45 % |
72238 |
0.19 % |
| mq40 |
546618 |
0.12 % |
407775 |
0.09 % |
138843 |
0.36 % |
| qd2,mq40 |
17981 |
0.00 % |
13568 |
0.00 % |
4413 |
0.01 % |
| fs60 |
1678 |
0.00 % |
0 |
0.00 % |
1678 |
0.00 % |
| q20,qd2,fs60 |
1133 |
0.00 % |
0 |
0.00 % |
1133 |
0.00 % |
| qd2,fs60 |
312 |
0.00 % |
0 |
0.00 % |
312 |
0.00 % |
| fs60,mq40 |
92 |
0.00 % |
0 |
0.00 % |
92 |
0.00 % |
| qd2,fs60,mq40 |
81 |
0.00 % |
0 |
0.00 % |
81 |
0.00 % |
| q20,fs60 |
37 |
0.00 % |
0 |
0.00 % |
37 |
0.00 % |
| q20,qd2,fs60,mq40 |
21 |
0.00 % |
0 |
0.00 % |
21 |
0.00 % |
| q20,fs60,mq40 |
2 |
0.00 % |
0 |
0.00 % |
2 |
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 |
19999771 |
32.59 % |
| Transition |
G>A |
All |
4664715 |
7.60 % |
| Transition |
T>C |
All |
21795153 |
35.52 % |
| Transition |
C>T |
All |
3293311 |
5.37 % |
| Transversion |
A>C |
All |
1311149 |
2.14 % |
| Transversion |
C>A |
All |
1916404 |
3.12 % |
| Transversion |
T>G |
All |
1433513 |
2.34 % |
| Transversion |
G>T |
All |
1814791 |
2.96 % |
| Transversion |
A>T |
All |
1581638 |
2.58 % |
| Transversion |
T>A |
All |
1767659 |
2.88 % |
| Transversion |
C>G |
All |
894985 |
1.46 % |
| Transversion |
G>C |
All |
892067 |
1.45 % |
| |
|
|
|
|
| Transition |
A>G |
Passed |
2513933 |
24.73 % |
| Transition |
G>A |
Passed |
900536 |
8.86 % |
| Transition |
T>C |
Passed |
4206266 |
41.38 % |
| Transition |
C>T |
Passed |
757287 |
7.45 % |
| Transversion |
A>C |
Passed |
227651 |
2.24 % |
| Transversion |
C>A |
Passed |
242991 |
2.39 % |
| Transversion |
T>G |
Passed |
234434 |
2.31 % |
| Transversion |
G>T |
Passed |
247184 |
2.43 % |
| Transversion |
A>T |
Passed |
180339 |
1.77 % |
| Transversion |
T>A |
Passed |
202620 |
1.99 % |
| Transversion |
C>G |
Passed |
222383 |
2.19 % |
| Transversion |
G>C |
Passed |
229640 |
2.26 % |
| |
|
|
|
|
| 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 |
4.28 |
49752950 |
11612206 |
| Passed |
4.69 |
8378022 |
1787242 |
| dbSNPAll |
0 |
0 |
0 |
| dbSNPPassed |
0 |
0 |
0 |