/EXTERNAL KNIH/variants/K006256_1_lane_gembs
BACK
SAMPLE K006256_1_lane_gembs
Variant counts
| Type |
Total |
Pass |
% |
| SNPs |
1202272377 |
413490626 |
34.39 % |
| Multiallelic |
0 |
0 |
0.00 % |
VCF Filtering Stats
| Type |
#Sites |
% |
#Non-Variant Sites |
% |
#Variant Sites |
% |
| All |
1202272377 |
100% |
1109672766 |
92.30 % |
92599611 |
7.70 % |
| |
|
|
|
|
|
|
| Passed |
436521782 |
36.31 % |
404125402 |
36.42 % |
32396380 |
7.42 % |
| Filtered |
765750595 |
63.69 % |
705547364 |
63.58 % |
60203231 |
13.79 % |
| |
|
|
|
|
|
|
| q20 |
675837760 |
88.26 % |
649658128 |
92.08 % |
26179632 |
43.49 % |
| q20,qd2 |
77304238 |
10.10 % |
44349131 |
6.29 % |
32955107 |
54.74 % |
| q20,mq40 |
5875571 |
0.77 % |
5685750 |
0.81 % |
189821 |
0.32 % |
| qd2 |
3250794 |
0.42 % |
2648255 |
0.38 % |
602539 |
1.00 % |
| q20,qd2,mq40 |
3032454 |
0.40 % |
2932910 |
0.42 % |
99544 |
0.17 % |
| mq40 |
435306 |
0.06 % |
262267 |
0.04 % |
173039 |
0.29 % |
| qd2,mq40 |
13985 |
0.00 % |
10923 |
0.00 % |
3062 |
0.01 % |
| fs60 |
219 |
0.00 % |
0 |
0.00 % |
219 |
0.00 % |
| q20,qd2,fs60 |
94 |
0.00 % |
0 |
0.00 % |
94 |
0.00 % |
| qd2,fs60 |
91 |
0.00 % |
0 |
0.00 % |
91 |
0.00 % |
| fs60,mq40 |
39 |
0.00 % |
0 |
0.00 % |
39 |
0.00 % |
| qd2,fs60,mq40 |
26 |
0.00 % |
0 |
0.00 % |
26 |
0.00 % |
| q20,qd2,fs60,mq40 |
16 |
0.00 % |
0 |
0.00 % |
16 |
0.00 % |
| q20,fs60 |
2 |
0.00 % |
0 |
0.00 % |
2 |
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 |
31861342 |
33.17 % |
| Transition |
G>A |
All |
4364209 |
4.54 % |
| Transition |
T>C |
All |
32010964 |
33.32 % |
| Transition |
C>T |
All |
3040128 |
3.16 % |
| Transversion |
A>C |
All |
3829457 |
3.99 % |
| Transversion |
C>A |
All |
3569624 |
3.72 % |
| Transversion |
T>G |
All |
4150305 |
4.32 % |
| Transversion |
G>T |
All |
3433309 |
3.57 % |
| Transversion |
A>T |
All |
2286019 |
2.38 % |
| Transversion |
T>A |
All |
2602332 |
2.71 % |
| Transversion |
C>G |
All |
2491881 |
2.59 % |
| Transversion |
G>C |
All |
2418739 |
2.52 % |
| |
|
|
|
|
| Transition |
A>G |
Passed |
2914874 |
29.95 % |
| Transition |
G>A |
Passed |
636059 |
6.54 % |
| Transition |
T>C |
Passed |
3523428 |
36.20 % |
| Transition |
C>T |
Passed |
430208 |
4.42 % |
| Transversion |
A>C |
Passed |
423382 |
4.35 % |
| Transversion |
C>A |
Passed |
270487 |
2.78 % |
| Transversion |
T>G |
Passed |
461577 |
4.74 % |
| Transversion |
G>T |
Passed |
220712 |
2.27 % |
| Transversion |
A>T |
Passed |
115018 |
1.18 % |
| Transversion |
T>A |
Passed |
172395 |
1.77 % |
| Transversion |
C>G |
Passed |
279890 |
2.88 % |
| Transversion |
G>C |
Passed |
284198 |
2.92 % |
| |
|
|
|
|
| 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 |
2.88 |
71276643 |
24781666 |
| Passed |
3.37 |
7504569 |
2227659 |
| dbSNPAll |
0 |
0 |
0 |
| dbSNPPassed |
0 |
0 |
0 |