/Martin Hirst/variants/PX0681_GGCTAC_3_lane_gembs
BACK
SAMPLE PX0681_GGCTAC_3_lane_gembs
Variant counts
| Type |
Total |
Pass |
% |
| SNPs |
1136091827 |
300712711 |
26.47 % |
| Multiallelic |
0 |
0 |
0.00 % |
VCF Filtering Stats
| Type |
#Sites |
% |
#Non-Variant Sites |
% |
#Variant Sites |
% |
| All |
1136091827 |
100% |
1063487885 |
93.61 % |
72603942 |
6.39 % |
| |
|
|
|
|
|
|
| Passed |
323164212 |
28.45 % |
296521206 |
27.88 % |
26643006 |
8.24 % |
| Filtered |
812927615 |
71.55 % |
766966679 |
72.12 % |
45960936 |
14.22 % |
| |
|
|
|
|
|
|
| q20 |
684858935 |
84.25 % |
668366408 |
87.14 % |
16492527 |
35.88 % |
| q20,qd2 |
101181888 |
12.45 % |
72574727 |
9.46 % |
28607161 |
62.24 % |
| q20,mq40 |
14417777 |
1.77 % |
14215126 |
1.85 % |
202651 |
0.44 % |
| q20,qd2,mq40 |
8513957 |
1.05 % |
8401580 |
1.10 % |
112377 |
0.24 % |
| qd2 |
3588908 |
0.44 % |
3266134 |
0.43 % |
322774 |
0.70 % |
| mq40 |
352400 |
0.04 % |
132565 |
0.02 % |
219835 |
0.48 % |
| qd2,mq40 |
13750 |
0.00 % |
10139 |
0.00 % |
3611 |
0.01 % |
| fs60 |
0 |
0.00 % |
0 |
0.00 % |
0 |
0.00 % |
| q20,fs60 |
0 |
0.00 % |
0 |
0.00 % |
0 |
0.00 % |
| qd2,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 |
14742844 |
19.22 % |
| Transition |
G>A |
All |
3800757 |
4.95 % |
| Transition |
T>C |
All |
15404552 |
20.08 % |
| Transition |
C>T |
All |
3798395 |
4.95 % |
| Transversion |
A>C |
All |
3618184 |
4.72 % |
| Transversion |
C>A |
All |
5134816 |
6.69 % |
| Transversion |
T>G |
All |
3442004 |
4.49 % |
| Transversion |
G>T |
All |
5267524 |
6.87 % |
| Transversion |
A>T |
All |
8219062 |
10.71 % |
| Transversion |
T>A |
All |
8149288 |
10.62 % |
| Transversion |
C>G |
All |
2487393 |
3.24 % |
| Transversion |
G>C |
All |
2648768 |
3.45 % |
| |
|
|
|
|
| Transition |
A>G |
Passed |
886640 |
20.85 % |
| Transition |
G>A |
Passed |
367065 |
8.63 % |
| Transition |
T>C |
Passed |
976089 |
22.95 % |
| Transition |
C>T |
Passed |
392031 |
9.22 % |
| Transversion |
A>C |
Passed |
267353 |
6.29 % |
| Transversion |
C>A |
Passed |
149059 |
3.50 % |
| Transversion |
T>G |
Passed |
244261 |
5.74 % |
| Transversion |
G>T |
Passed |
163476 |
3.84 % |
| Transversion |
A>T |
Passed |
165515 |
3.89 % |
| Transversion |
T>A |
Passed |
148244 |
3.49 % |
| Transversion |
C>G |
Passed |
235473 |
5.54 % |
| Transversion |
G>C |
Passed |
257847 |
6.06 % |
| |
|
|
|
|
| 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 |
0.97 |
37746548 |
38967039 |
| Passed |
1.61 |
2621825 |
1631228 |
| dbSNPAll |
0 |
0 |
0 |
| dbSNPPassed |
0 |
0 |
0 |