/Martin Hirst/variants/PX0821_ACCCAG_6_lane_gembs
BACK
SAMPLE PX0821_ACCCAG_6_lane_gembs
Variant counts
| Type |
Total |
Pass |
% |
| SNPs |
1223153761 |
770935550 |
63.03 % |
| Multiallelic |
0 |
0 |
0.00 % |
VCF Filtering Stats
| Type |
#Sites |
% |
#Non-Variant Sites |
% |
#Variant Sites |
% |
| All |
1223153761 |
100% |
1138629359 |
93.09 % |
84524402 |
6.91 % |
| |
|
|
|
|
|
|
| Passed |
787546383 |
64.39 % |
763081901 |
67.02 % |
24464482 |
3.11 % |
| Filtered |
435607378 |
35.61 % |
375547458 |
32.98 % |
60059920 |
7.63 % |
| |
|
|
|
|
|
|
| q20 |
347725842 |
79.83 % |
332236310 |
88.47 % |
15489532 |
25.79 % |
| q20,qd2 |
64619110 |
14.83 % |
21749945 |
5.79 % |
42869165 |
71.38 % |
| qd2 |
14045938 |
3.22 % |
12877558 |
3.43 % |
1168380 |
1.95 % |
| q20,mq40 |
6113700 |
1.40 % |
5939477 |
1.58 % |
174223 |
0.29 % |
| q20,qd2,mq40 |
2534734 |
0.58 % |
2393307 |
0.64 % |
141427 |
0.24 % |
| mq40 |
547054 |
0.13 % |
335191 |
0.09 % |
211863 |
0.35 % |
| qd2,mq40 |
20991 |
0.00 % |
15670 |
0.00 % |
5321 |
0.01 % |
| qd2,fs60 |
8 |
0.00 % |
0 |
0.00 % |
8 |
0.00 % |
| fs60 |
1 |
0.00 % |
0 |
0.00 % |
1 |
0.00 % |
| q20,fs60 |
0 |
0.00 % |
0 |
0.00 % |
0 |
0.00 % |
| q20,qd2,fs60 |
0 |
0.00 % |
0 |
0.00 % |
0 |
0.00 % |
| fs60,mq40 |
0 |
0.00 % |
0 |
0.00 % |
0 |
0.00 % |
| q20,fs60,mq40 |
0 |
0.00 % |
0 |
0.00 % |
0 |
0.00 % |
| qd2,fs60,mq40 |
0 |
0.00 % |
0 |
0.00 % |
0 |
0.00 % |
| q20,qd2,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 |
21904181 |
25.54 % |
| Transition |
G>A |
All |
5245513 |
6.12 % |
| Transition |
T>C |
All |
21352423 |
24.89 % |
| Transition |
C>T |
All |
5341612 |
6.23 % |
| Transversion |
A>C |
All |
3050356 |
3.56 % |
| Transversion |
C>A |
All |
3691913 |
4.30 % |
| Transversion |
T>G |
All |
3008327 |
3.51 % |
| Transversion |
G>T |
All |
3780004 |
4.41 % |
| Transversion |
A>T |
All |
7532596 |
8.78 % |
| Transversion |
T>A |
All |
7350939 |
8.57 % |
| Transversion |
C>G |
All |
1755561 |
2.05 % |
| Transversion |
G>C |
All |
1762625 |
2.05 % |
| |
|
|
|
|
| Transition |
A>G |
Passed |
1913416 |
23.83 % |
| Transition |
G>A |
Passed |
776376 |
9.67 % |
| Transition |
T>C |
Passed |
1915865 |
23.87 % |
| Transition |
C>T |
Passed |
801190 |
9.98 % |
| Transversion |
A>C |
Passed |
422460 |
5.26 % |
| Transversion |
C>A |
Passed |
260780 |
3.25 % |
| Transversion |
T>G |
Passed |
401112 |
5.00 % |
| Transversion |
G>T |
Passed |
270253 |
3.37 % |
| Transversion |
A>T |
Passed |
306535 |
3.82 % |
| Transversion |
T>A |
Passed |
287866 |
3.59 % |
| Transversion |
C>G |
Passed |
331478 |
4.13 % |
| Transversion |
G>C |
Passed |
340466 |
4.24 % |
| |
|
|
|
|
| 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 |
1.69 |
53843729 |
31932321 |
| Passed |
2.06 |
5406847 |
2620950 |
| dbSNPAll |
0 |
0 |
0 |
| dbSNPPassed |
0 |
0 |
0 |