/EXTERNAL BLUEPRINT/variants/K006366_20_lane_gembs
BACK
SAMPLE K006366_20_lane_gembs
Variant counts
| Type |
Total |
Pass |
% |
| SNPs |
1143990132 |
717610109 |
62.73 % |
| Multiallelic |
0 |
0 |
0.00 % |
VCF Filtering Stats
| Type |
#Sites |
% |
#Non-Variant Sites |
% |
#Variant Sites |
% |
| All |
1143990132 |
100% |
1124989585 |
98.34 % |
19000547 |
1.66 % |
| |
|
|
|
|
|
|
| Passed |
719542884 |
62.90 % |
715576266 |
63.61 % |
3966618 |
0.55 % |
| Filtered |
424447248 |
37.10 % |
409413319 |
36.39 % |
15033929 |
2.09 % |
| |
|
|
|
|
|
|
| q20 |
358990443 |
84.58 % |
356118771 |
86.98 % |
2871672 |
19.10 % |
| q20,qd2 |
36598046 |
8.62 % |
25240453 |
6.17 % |
11357593 |
75.55 % |
| q20,mq40 |
14638114 |
3.45 % |
14457943 |
3.53 % |
180171 |
1.20 % |
| mq40 |
7221095 |
1.70 % |
7018651 |
1.71 % |
202444 |
1.35 % |
| q20,qd2,mq40 |
3574589 |
0.84 % |
3296226 |
0.81 % |
278363 |
1.85 % |
| qd2 |
3312334 |
0.78 % |
3188711 |
0.78 % |
123623 |
0.82 % |
| qd2,mq40 |
105762 |
0.02 % |
92564 |
0.02 % |
13198 |
0.09 % |
| q20,qd2,fs60 |
2082 |
0.00 % |
0 |
0.00 % |
2082 |
0.01 % |
| qd2,fs60,mq40 |
1448 |
0.00 % |
0 |
0.00 % |
1448 |
0.01 % |
| fs60 |
1313 |
0.00 % |
0 |
0.00 % |
1313 |
0.01 % |
| qd2,fs60 |
945 |
0.00 % |
0 |
0.00 % |
945 |
0.01 % |
| fs60,mq40 |
586 |
0.00 % |
0 |
0.00 % |
586 |
0.00 % |
| q20,qd2,fs60,mq40 |
486 |
0.00 % |
0 |
0.00 % |
486 |
0.00 % |
| q20,fs60,mq40 |
3 |
0.00 % |
0 |
0.00 % |
3 |
0.00 % |
| q20,fs60 |
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 |
3805649 |
16.97 % |
| Transition |
G>A |
All |
4793075 |
21.37 % |
| Transition |
T>C |
All |
3735429 |
16.66 % |
| Transition |
C>T |
All |
4756843 |
21.21 % |
| Transversion |
A>C |
All |
406385 |
1.81 % |
| Transversion |
C>A |
All |
971814 |
4.33 % |
| Transversion |
T>G |
All |
409837 |
1.83 % |
| Transversion |
G>T |
All |
992188 |
4.42 % |
| Transversion |
A>T |
All |
1000337 |
4.46 % |
| Transversion |
T>A |
All |
966254 |
4.31 % |
| Transversion |
C>G |
All |
296849 |
1.32 % |
| Transversion |
G>C |
All |
292237 |
1.30 % |
| |
|
|
|
|
| Transition |
A>G |
Passed |
499942 |
17.81 % |
| Transition |
G>A |
Passed |
482280 |
17.18 % |
| Transition |
T>C |
Passed |
498749 |
17.76 % |
| Transition |
C>T |
Passed |
483579 |
17.22 % |
| Transversion |
A>C |
Passed |
110774 |
3.95 % |
| Transversion |
C>A |
Passed |
106193 |
3.78 % |
| Transversion |
T>G |
Passed |
110372 |
3.93 % |
| Transversion |
G>T |
Passed |
106721 |
3.80 % |
| Transversion |
A>T |
Passed |
76341 |
2.72 % |
| Transversion |
T>A |
Passed |
76748 |
2.73 % |
| Transversion |
C>G |
Passed |
127679 |
4.55 % |
| Transversion |
G>C |
Passed |
128333 |
4.57 % |
| |
|
|
|
|
| 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 |
3.20 |
17090996 |
5335901 |
| Passed |
2.33 |
1964550 |
843161 |
| dbSNPAll |
0 |
0 |
0 |
| dbSNPPassed |
0 |
0 |
0 |