/EXTERNAL DEEP/variants/K009049_K009050_K009051_K009052_K009053_K009054_K009055_K009056_K009057_K009058_K009059_K009060_K009061_K009062_K009063_K009064_K009065_17_lane_gembs
BACK
SAMPLE K009049_K009050_K009051_K009052_K009053_K009054_K009055_K009056_K009057_K009058_K009059_K009060_K009061_K009062_K009063_K009064_K009065_17_lane_gembs
Variant counts
| Type |
Total |
Pass |
% |
| SNPs |
1188869932 |
853161780 |
71.76 % |
| Multiallelic |
0 |
0 |
0.00 % |
VCF Filtering Stats
| Type |
#Sites |
% |
#Non-Variant Sites |
% |
#Variant Sites |
% |
| All |
1188869932 |
100% |
1140828356 |
95.96 % |
48041576 |
4.04 % |
| |
|
|
|
|
|
|
| Passed |
860275165 |
72.36 % |
847717135 |
74.31 % |
12558030 |
1.46 % |
| Filtered |
328594767 |
27.64 % |
293111221 |
25.69 % |
35483546 |
4.12 % |
| |
|
|
|
|
|
|
| q20 |
261444636 |
79.56 % |
252815924 |
86.25 % |
8628712 |
24.32 % |
| q20,qd2 |
39492100 |
12.02 % |
14635382 |
4.99 % |
24856718 |
70.05 % |
| q20,mq40 |
11513279 |
3.50 % |
11141462 |
3.80 % |
371817 |
1.05 % |
| qd2 |
10277185 |
3.13 % |
9523270 |
3.25 % |
753915 |
2.12 % |
| q20,qd2,mq40 |
3670090 |
1.12 % |
3285578 |
1.12 % |
384512 |
1.08 % |
| mq40 |
2123153 |
0.65 % |
1650675 |
0.56 % |
472478 |
1.33 % |
| qd2,mq40 |
71545 |
0.02 % |
58930 |
0.02 % |
12615 |
0.04 % |
| qd2,fs60,mq40 |
810 |
0.00 % |
0 |
0.00 % |
810 |
0.00 % |
| q20,qd2,fs60 |
612 |
0.00 % |
0 |
0.00 % |
612 |
0.00 % |
| qd2,fs60 |
550 |
0.00 % |
0 |
0.00 % |
550 |
0.00 % |
| fs60 |
375 |
0.00 % |
0 |
0.00 % |
375 |
0.00 % |
| fs60,mq40 |
300 |
0.00 % |
0 |
0.00 % |
300 |
0.00 % |
| q20,qd2,fs60,mq40 |
131 |
0.00 % |
0 |
0.00 % |
131 |
0.00 % |
| q20,fs60 |
1 |
0.00 % |
0 |
0.00 % |
1 |
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 |
16198821 |
32.28 % |
| Transition |
G>A |
All |
3755444 |
7.48 % |
| Transition |
T>C |
All |
18408671 |
36.69 % |
| Transition |
C>T |
All |
3124487 |
6.23 % |
| Transversion |
A>C |
All |
552917 |
1.10 % |
| Transversion |
C>A |
All |
1952652 |
3.89 % |
| Transversion |
T>G |
All |
612618 |
1.22 % |
| Transversion |
G>T |
All |
1911401 |
3.81 % |
| Transversion |
A>T |
All |
1348162 |
2.69 % |
| Transversion |
T>A |
All |
1365361 |
2.72 % |
| Transversion |
C>G |
All |
481458 |
0.96 % |
| Transversion |
G>C |
All |
463772 |
0.92 % |
| |
|
|
|
|
| Transition |
A>G |
Passed |
1239327 |
19.70 % |
| Transition |
G>A |
Passed |
664129 |
10.55 % |
| Transition |
T>C |
Passed |
2269862 |
36.07 % |
| Transition |
C>T |
Passed |
598323 |
9.51 % |
| Transversion |
A>C |
Passed |
164623 |
2.62 % |
| Transversion |
C>A |
Passed |
279135 |
4.44 % |
| Transversion |
T>G |
Passed |
174790 |
2.78 % |
| Transversion |
G>T |
Passed |
255630 |
4.06 % |
| Transversion |
A>T |
Passed |
147310 |
2.34 % |
| Transversion |
T>A |
Passed |
167091 |
2.66 % |
| Transversion |
C>G |
Passed |
167128 |
2.66 % |
| Transversion |
G>C |
Passed |
164842 |
2.62 % |
| |
|
|
|
|
| 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 |
4.78 |
41487423 |
8688341 |
| Passed |
3.14 |
4771641 |
1520549 |
| dbSNPAll |
0 |
0 |
0 |
| dbSNPPassed |
0 |
0 |
0 |