/EXTERNAL BLUEPRINT/variants/K006429_22_lane_gembs
BACK
SAMPLE K006429_22_lane_gembs
Variant counts
| Type |
Total |
Pass |
% |
| SNPs |
1156568697 |
924913101 |
79.97 % |
| Multiallelic |
0 |
0 |
0.00 % |
VCF Filtering Stats
| Type |
#Sites |
% |
#Non-Variant Sites |
% |
#Variant Sites |
% |
| All |
1156568697 |
100% |
1143206032 |
98.84 % |
13362665 |
1.16 % |
| |
|
|
|
|
|
|
| Passed |
927071460 |
80.16 % |
922713922 |
80.71 % |
4357538 |
0.47 % |
| Filtered |
229497237 |
19.84 % |
220492110 |
19.29 % |
9005127 |
0.97 % |
| |
|
|
|
|
|
|
| q20 |
193507069 |
84.32 % |
192206041 |
87.17 % |
1301028 |
14.45 % |
| q20,mq40 |
13702669 |
5.97 % |
13598567 |
6.17 % |
104102 |
1.16 % |
| q20,qd2 |
12670284 |
5.52 % |
5495068 |
2.49 % |
7175216 |
79.68 % |
| mq40 |
4533477 |
1.98 % |
4353331 |
1.97 % |
180146 |
2.00 % |
| q20,qd2,mq40 |
2984222 |
1.30 % |
2821010 |
1.28 % |
163212 |
1.81 % |
| qd2 |
2054969 |
0.90 % |
1982446 |
0.90 % |
72523 |
0.81 % |
| qd2,mq40 |
43140 |
0.02 % |
35647 |
0.02 % |
7493 |
0.08 % |
| qd2,fs60,mq40 |
604 |
0.00 % |
0 |
0.00 % |
604 |
0.01 % |
| fs60,mq40 |
316 |
0.00 % |
0 |
0.00 % |
316 |
0.00 % |
| qd2,fs60 |
206 |
0.00 % |
0 |
0.00 % |
206 |
0.00 % |
| fs60 |
152 |
0.00 % |
0 |
0.00 % |
152 |
0.00 % |
| q20,qd2,fs60,mq40 |
79 |
0.00 % |
0 |
0.00 % |
79 |
0.00 % |
| q20,qd2,fs60 |
48 |
0.00 % |
0 |
0.00 % |
48 |
0.00 % |
| q20,fs60,mq40 |
2 |
0.00 % |
0 |
0.00 % |
2 |
0.00 % |
| q20,fs60 |
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 |
4998939 |
33.21 % |
| Transition |
G>A |
All |
1042737 |
6.93 % |
| Transition |
T>C |
All |
4944045 |
32.85 % |
| Transition |
C>T |
All |
1054538 |
7.01 % |
| Transversion |
A>C |
All |
234190 |
1.56 % |
| Transversion |
C>A |
All |
632387 |
4.20 % |
| Transversion |
T>G |
All |
236136 |
1.57 % |
| Transversion |
G>T |
All |
629557 |
4.18 % |
| Transversion |
A>T |
All |
435760 |
2.89 % |
| Transversion |
T>A |
All |
426993 |
2.84 % |
| Transversion |
C>G |
All |
208570 |
1.39 % |
| Transversion |
G>C |
All |
208582 |
1.39 % |
| |
|
|
|
|
| Transition |
A>G |
Passed |
550850 |
17.25 % |
| Transition |
G>A |
Passed |
520861 |
16.31 % |
| Transition |
T>C |
Passed |
551768 |
17.28 % |
| Transition |
C>T |
Passed |
523623 |
16.40 % |
| Transversion |
A>C |
Passed |
135063 |
4.23 % |
| Transversion |
C>A |
Passed |
136188 |
4.27 % |
| Transversion |
T>G |
Passed |
135131 |
4.23 % |
| Transversion |
G>T |
Passed |
136591 |
4.28 % |
| Transversion |
A>T |
Passed |
110593 |
3.46 % |
| Transversion |
T>A |
Passed |
110784 |
3.47 % |
| Transversion |
C>G |
Passed |
140016 |
4.39 % |
| Transversion |
G>C |
Passed |
141075 |
4.42 % |
| |
|
|
|
|
| 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 |
4.00 |
12040259 |
3012175 |
| Passed |
2.05 |
2147102 |
1045441 |
| dbSNPAll |
0 |
0 |
0 |
| dbSNPPassed |
0 |
0 |
0 |