/EXTERNAL BLUEPRINT/variants/K006336_5_lane_gembs
BACK
SAMPLE K006336_5_lane_gembs
Variant counts
| Type |
Total |
Pass |
% |
| SNPs |
1137354219 |
810686266 |
71.28 % |
| Multiallelic |
0 |
0 |
0.00 % |
VCF Filtering Stats
| Type |
#Sites |
% |
#Non-Variant Sites |
% |
#Variant Sites |
% |
| All |
1137354219 |
100% |
1117505778 |
98.25 % |
19848441 |
1.75 % |
| |
|
|
|
|
|
|
| Passed |
812169804 |
71.41 % |
808971368 |
72.39 % |
3198436 |
0.39 % |
| Filtered |
325184415 |
28.59 % |
308534410 |
27.61 % |
16650005 |
2.05 % |
| |
|
|
|
|
|
|
| q20 |
260438871 |
80.09 % |
258800547 |
83.88 % |
1638324 |
9.84 % |
| q20,qd2 |
37391385 |
11.50 % |
23069618 |
7.48 % |
14321767 |
86.02 % |
| q20,mq40 |
12463747 |
3.83 % |
12350177 |
4.00 % |
113570 |
0.68 % |
| mq40 |
8955244 |
2.75 % |
8764183 |
2.84 % |
191061 |
1.15 % |
| qd2 |
3025512 |
0.93 % |
2896515 |
0.94 % |
128997 |
0.77 % |
| q20,qd2,mq40 |
2772873 |
0.85 % |
2545610 |
0.83 % |
227263 |
1.36 % |
| qd2,mq40 |
123598 |
0.04 % |
107760 |
0.03 % |
15838 |
0.10 % |
| q20,qd2,fs60 |
5698 |
0.00 % |
0 |
0.00 % |
5698 |
0.03 % |
| fs60 |
2590 |
0.00 % |
0 |
0.00 % |
2590 |
0.02 % |
| qd2,fs60,mq40 |
1836 |
0.00 % |
0 |
0.00 % |
1836 |
0.01 % |
| qd2,fs60 |
1573 |
0.00 % |
0 |
0.00 % |
1573 |
0.01 % |
| fs60,mq40 |
768 |
0.00 % |
0 |
0.00 % |
768 |
0.00 % |
| q20,qd2,fs60,mq40 |
706 |
0.00 % |
0 |
0.00 % |
706 |
0.00 % |
| q20,fs60 |
7 |
0.00 % |
0 |
0.00 % |
7 |
0.00 % |
| q20,fs60,mq40 |
7 |
0.00 % |
0 |
0.00 % |
7 |
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 |
3290326 |
12.17 % |
| Transition |
G>A |
All |
9032431 |
33.40 % |
| Transition |
T>C |
All |
3036544 |
11.23 % |
| Transition |
C>T |
All |
8865813 |
32.78 % |
| Transversion |
A>C |
All |
222900 |
0.82 % |
| Transversion |
C>A |
All |
568332 |
2.10 % |
| Transversion |
T>G |
All |
238417 |
0.88 % |
| Transversion |
G>T |
All |
560071 |
2.07 % |
| Transversion |
A>T |
All |
419671 |
1.55 % |
| Transversion |
T>A |
All |
420390 |
1.55 % |
| Transversion |
C>G |
All |
199278 |
0.74 % |
| Transversion |
G>C |
All |
192405 |
0.71 % |
| |
|
|
|
|
| Transition |
A>G |
Passed |
466039 |
18.15 % |
| Transition |
G>A |
Passed |
438114 |
17.06 % |
| Transition |
T>C |
Passed |
465329 |
18.12 % |
| Transition |
C>T |
Passed |
438718 |
17.08 % |
| Transversion |
A>C |
Passed |
100886 |
3.93 % |
| Transversion |
C>A |
Passed |
94839 |
3.69 % |
| Transversion |
T>G |
Passed |
100860 |
3.93 % |
| Transversion |
G>T |
Passed |
95110 |
3.70 % |
| Transversion |
A>T |
Passed |
70311 |
2.74 % |
| Transversion |
T>A |
Passed |
70409 |
2.74 % |
| Transversion |
C>G |
Passed |
113317 |
4.41 % |
| Transversion |
G>C |
Passed |
113962 |
4.44 % |
| |
|
|
|
|
| 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 |
8.59 |
24225114 |
2821464 |
| Passed |
2.38 |
1808200 |
759694 |
| dbSNPAll |
0 |
0 |
0 |
| dbSNPPassed |
0 |
0 |
0 |