/Martin Hirst/variants/PX0720_CCGTCC_10_lane_gembs
BACK
SAMPLE PX0720_CCGTCC_10_lane_gembs
Variant counts
| Type |
Total |
Pass |
% |
| SNPs |
1190708556 |
550334295 |
46.22 % |
| Multiallelic |
0 |
0 |
0.00 % |
VCF Filtering Stats
| Type |
#Sites |
% |
#Non-Variant Sites |
% |
#Variant Sites |
% |
| All |
1190708556 |
100% |
1107479748 |
93.01 % |
83228808 |
6.99 % |
| |
|
|
|
|
|
|
| Passed |
571885635 |
48.03 % |
545519473 |
49.26 % |
26366162 |
4.61 % |
| Filtered |
618822921 |
51.97 % |
561960275 |
50.74 % |
56862646 |
9.94 % |
| |
|
|
|
|
|
|
| q20 |
509066684 |
82.26 % |
489349325 |
87.08 % |
19717359 |
34.68 % |
| q20,qd2 |
81437569 |
13.16 % |
45723140 |
8.14 % |
35714429 |
62.81 % |
| qd2 |
11082061 |
1.79 % |
10322469 |
1.84 % |
759592 |
1.34 % |
| q20,mq40 |
10925058 |
1.77 % |
10683501 |
1.90 % |
241557 |
0.42 % |
| q20,qd2,mq40 |
5661636 |
0.91 % |
5502428 |
0.98 % |
159208 |
0.28 % |
| mq40 |
620131 |
0.10 % |
356800 |
0.06 % |
263331 |
0.46 % |
| qd2,mq40 |
29777 |
0.00 % |
22612 |
0.00 % |
7165 |
0.01 % |
| qd2,fs60 |
3 |
0.00 % |
0 |
0.00 % |
3 |
0.00 % |
| fs60,mq40 |
1 |
0.00 % |
0 |
0.00 % |
1 |
0.00 % |
| qd2,fs60,mq40 |
1 |
0.00 % |
0 |
0.00 % |
1 |
0.00 % |
| fs60 |
0 |
0.00 % |
0 |
0.00 % |
0 |
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 % |
| q20,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 |
20419089 |
23.49 % |
| Transition |
G>A |
All |
4386166 |
5.05 % |
| Transition |
T>C |
All |
20146438 |
23.18 % |
| Transition |
C>T |
All |
4493168 |
5.17 % |
| Transversion |
A>C |
All |
3794663 |
4.37 % |
| Transversion |
C>A |
All |
4449995 |
5.12 % |
| Transversion |
T>G |
All |
3691910 |
4.25 % |
| Transversion |
G>T |
All |
4534870 |
5.22 % |
| Transversion |
A>T |
All |
8333769 |
9.59 % |
| Transversion |
T>A |
All |
8245406 |
9.49 % |
| Transversion |
C>G |
All |
2191260 |
2.52 % |
| Transversion |
G>C |
All |
2239787 |
2.58 % |
| |
|
|
|
|
| Transition |
A>G |
Passed |
1328200 |
25.39 % |
| Transition |
G>A |
Passed |
436517 |
8.34 % |
| Transition |
T>C |
Passed |
1376261 |
26.31 % |
| Transition |
C>T |
Passed |
450600 |
8.61 % |
| Transversion |
A>C |
Passed |
281447 |
5.38 % |
| Transversion |
C>A |
Passed |
146723 |
2.80 % |
| Transversion |
T>G |
Passed |
265740 |
5.08 % |
| Transversion |
G>T |
Passed |
153367 |
2.93 % |
| Transversion |
A>T |
Passed |
178001 |
3.40 % |
| Transversion |
T>A |
Passed |
166319 |
3.18 % |
| Transversion |
C>G |
Passed |
218847 |
4.18 % |
| Transversion |
G>C |
Passed |
229255 |
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 |
1.32 |
49444861 |
37481660 |
| Passed |
2.19 |
3591578 |
1639699 |
| dbSNPAll |
0 |
0 |
0 |
| dbSNPPassed |
0 |
0 |
0 |