/Martin Hirst/variants/PX0821_AACCCC_6_lane_gembs
BACK
SAMPLE PX0821_AACCCC_6_lane_gembs
Variant counts
| Type |
Total |
Pass |
% |
| SNPs |
1224350658 |
693235028 |
56.62 % |
| Multiallelic |
0 |
0 |
0.00 % |
VCF Filtering Stats
| Type |
#Sites |
% |
#Non-Variant Sites |
% |
#Variant Sites |
% |
| All |
1224350658 |
100% |
1135760977 |
92.76 % |
88589681 |
7.24 % |
| |
|
|
|
|
|
|
| Passed |
711896432 |
58.14 % |
685792130 |
60.38 % |
26104302 |
3.67 % |
| Filtered |
512454226 |
41.86 % |
449968847 |
39.62 % |
62485379 |
8.78 % |
| |
|
|
|
|
|
|
| q20 |
425395004 |
83.01 % |
408458178 |
90.77 % |
16936826 |
27.11 % |
| q20,qd2 |
67279857 |
13.13 % |
23071491 |
5.13 % |
44208366 |
70.75 % |
| qd2 |
10688685 |
2.09 % |
9836151 |
2.19 % |
852534 |
1.36 % |
| q20,mq40 |
6022912 |
1.18 % |
5860456 |
1.30 % |
162456 |
0.26 % |
| q20,qd2,mq40 |
2586094 |
0.50 % |
2458872 |
0.55 % |
127222 |
0.20 % |
| mq40 |
463848 |
0.09 % |
270418 |
0.06 % |
193430 |
0.31 % |
| qd2,mq40 |
17819 |
0.00 % |
13281 |
0.00 % |
4538 |
0.01 % |
| qd2,fs60 |
6 |
0.00 % |
0 |
0.00 % |
6 |
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 |
22032077 |
24.50 % |
| Transition |
G>A |
All |
5265745 |
5.86 % |
| Transition |
T>C |
All |
21245449 |
23.62 % |
| Transition |
C>T |
All |
5361445 |
5.96 % |
| Transversion |
A>C |
All |
3312788 |
3.68 % |
| Transversion |
C>A |
All |
4271183 |
4.75 % |
| Transversion |
T>G |
All |
3318565 |
3.69 % |
| Transversion |
G>T |
All |
4376777 |
4.87 % |
| Transversion |
A>T |
All |
8452439 |
9.40 % |
| Transversion |
T>A |
All |
8270261 |
9.20 % |
| Transversion |
C>G |
All |
2012007 |
2.24 % |
| Transversion |
G>C |
All |
2010787 |
2.24 % |
| |
|
|
|
|
| Transition |
A>G |
Passed |
1770348 |
23.29 % |
| Transition |
G>A |
Passed |
716729 |
9.43 % |
| Transition |
T>C |
Passed |
1758285 |
23.13 % |
| Transition |
C>T |
Passed |
743673 |
9.78 % |
| Transversion |
A>C |
Passed |
418983 |
5.51 % |
| Transversion |
C>A |
Passed |
255994 |
3.37 % |
| Transversion |
T>G |
Passed |
403596 |
5.31 % |
| Transversion |
G>T |
Passed |
268389 |
3.53 % |
| Transversion |
A>T |
Passed |
300757 |
3.96 % |
| Transversion |
T>A |
Passed |
280096 |
3.68 % |
| Transversion |
C>G |
Passed |
337175 |
4.44 % |
| Transversion |
G>C |
Passed |
347933 |
4.58 % |
| |
|
|
|
|
| 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 |
1.50 |
53904716 |
36024807 |
| Passed |
1.91 |
4989035 |
2612923 |
| dbSNPAll |
0 |
0 |
0 |
| dbSNPPassed |
0 |
0 |
0 |