/EXTERNAL BLUEPRINT/variants/K006270_8_lane_gembs
BACK
SAMPLE K006270_8_lane_gembs
Variant counts
| Type |
Total |
Pass |
% |
| SNPs |
1145205213 |
833023774 |
72.74 % |
| Multiallelic |
0 |
0 |
0.00 % |
VCF Filtering Stats
| Type |
#Sites |
% |
#Non-Variant Sites |
% |
#Variant Sites |
% |
| All |
1145205213 |
100% |
1126978682 |
98.41 % |
18226531 |
1.59 % |
| |
|
|
|
|
|
|
| Passed |
834206701 |
72.84 % |
831359642 |
73.77 % |
2847059 |
0.34 % |
| Filtered |
310998512 |
27.16 % |
295619040 |
26.23 % |
15379472 |
1.84 % |
| |
|
|
|
|
|
|
| q20 |
241467745 |
77.64 % |
239849018 |
81.13 % |
1618727 |
10.53 % |
| q20,qd2 |
34420500 |
11.07 % |
21370960 |
7.23 % |
13049540 |
84.85 % |
| q20,mq40 |
12186406 |
3.92 % |
12070270 |
4.08 % |
116136 |
0.76 % |
| qd2 |
10928659 |
3.51 % |
10782446 |
3.65 % |
146213 |
0.95 % |
| mq40 |
9048117 |
2.91 % |
8847008 |
2.99 % |
201109 |
1.31 % |
| q20,qd2,mq40 |
2771207 |
0.89 % |
2560145 |
0.87 % |
211062 |
1.37 % |
| qd2,mq40 |
156990 |
0.05 % |
139193 |
0.05 % |
17797 |
0.12 % |
| q20,qd2,fs60 |
7295 |
0.00 % |
0 |
0.00 % |
7295 |
0.05 % |
| fs60 |
3927 |
0.00 % |
0 |
0.00 % |
3927 |
0.03 % |
| qd2,fs60 |
3150 |
0.00 % |
0 |
0.00 % |
3150 |
0.02 % |
| qd2,fs60,mq40 |
2730 |
0.00 % |
0 |
0.00 % |
2730 |
0.02 % |
| fs60,mq40 |
936 |
0.00 % |
0 |
0.00 % |
936 |
0.01 % |
| q20,qd2,fs60,mq40 |
827 |
0.00 % |
0 |
0.00 % |
827 |
0.01 % |
| q20,fs60 |
16 |
0.00 % |
0 |
0.00 % |
16 |
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 |
2747699 |
8.48 % |
| Transition |
G>A |
All |
12304589 |
37.99 % |
| Transition |
T>C |
All |
2644229 |
8.16 % |
| Transition |
C>T |
All |
12292054 |
37.95 % |
| Transversion |
A>C |
All |
213439 |
0.66 % |
| Transversion |
C>A |
All |
444339 |
1.37 % |
| Transversion |
T>G |
All |
222035 |
0.69 % |
| Transversion |
G>T |
All |
440554 |
1.36 % |
| Transversion |
A>T |
All |
352481 |
1.09 % |
| Transversion |
T>A |
All |
343183 |
1.06 % |
| Transversion |
C>G |
All |
197818 |
0.61 % |
| Transversion |
G>C |
All |
190019 |
0.59 % |
| |
|
|
|
|
| Transition |
A>G |
Passed |
465448 |
18.09 % |
| Transition |
G>A |
Passed |
441499 |
17.16 % |
| Transition |
T>C |
Passed |
465658 |
18.10 % |
| Transition |
C>T |
Passed |
440814 |
17.14 % |
| Transversion |
A>C |
Passed |
100060 |
3.89 % |
| Transversion |
C>A |
Passed |
94699 |
3.68 % |
| Transversion |
T>G |
Passed |
100046 |
3.89 % |
| Transversion |
G>T |
Passed |
94493 |
3.67 % |
| Transversion |
A>T |
Passed |
72141 |
2.80 % |
| Transversion |
T>A |
Passed |
72000 |
2.80 % |
| Transversion |
C>G |
Passed |
112908 |
4.39 % |
| Transversion |
G>C |
Passed |
112575 |
4.38 % |
| |
|
|
|
|
| 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 |
12.48 |
29988571 |
2403868 |
| Passed |
2.39 |
1813419 |
758922 |
| dbSNPAll |
0 |
0 |
0 |
| dbSNPPassed |
0 |
0 |
0 |