/Martin Hirst/variants/PX0821_GATCAG_6_lane_gembs
BACK
SAMPLE PX0821_GATCAG_6_lane_gembs
Variant counts
| Type |
Total |
Pass |
% |
| SNPs |
1223967414 |
776557155 |
63.45 % |
| Multiallelic |
0 |
0 |
0.00 % |
VCF Filtering Stats
| Type |
#Sites |
% |
#Non-Variant Sites |
% |
#Variant Sites |
% |
| All |
1223967414 |
100% |
1138363350 |
93.01 % |
85604064 |
6.99 % |
| |
|
|
|
|
|
|
| Passed |
793612359 |
64.84 % |
768621414 |
67.52 % |
24990945 |
3.15 % |
| Filtered |
430355055 |
35.16 % |
369741936 |
32.48 % |
60613119 |
7.64 % |
| |
|
|
|
|
|
|
| q20 |
339122941 |
78.80 % |
323010155 |
87.36 % |
16112786 |
26.58 % |
| q20,qd2 |
65447444 |
15.21 % |
22851874 |
6.18 % |
42595570 |
70.27 % |
| qd2 |
16079665 |
3.74 % |
14757333 |
3.99 % |
1322332 |
2.18 % |
| q20,mq40 |
6398978 |
1.49 % |
6209563 |
1.68 % |
189415 |
0.31 % |
| q20,qd2,mq40 |
2677570 |
0.62 % |
2520330 |
0.68 % |
157240 |
0.26 % |
| mq40 |
605541 |
0.14 % |
375434 |
0.10 % |
230107 |
0.38 % |
| qd2,mq40 |
22907 |
0.01 % |
17247 |
0.00 % |
5660 |
0.01 % |
| qd2,fs60 |
5 |
0.00 % |
0 |
0.00 % |
5 |
0.00 % |
| fs60 |
3 |
0.00 % |
0 |
0.00 % |
3 |
0.00 % |
| q20,qd2,fs60 |
1 |
0.00 % |
0 |
0.00 % |
1 |
0.00 % |
| q20,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 |
22318153 |
25.66 % |
| Transition |
G>A |
All |
5217095 |
6.00 % |
| Transition |
T>C |
All |
21825764 |
25.09 % |
| Transition |
C>T |
All |
5324660 |
6.12 % |
| Transversion |
A>C |
All |
3110922 |
3.58 % |
| Transversion |
C>A |
All |
3714937 |
4.27 % |
| Transversion |
T>G |
All |
3055080 |
3.51 % |
| Transversion |
G>T |
All |
3804849 |
4.37 % |
| Transversion |
A>T |
All |
7640128 |
8.78 % |
| Transversion |
T>A |
All |
7442235 |
8.56 % |
| Transversion |
C>G |
All |
1761465 |
2.03 % |
| Transversion |
G>C |
All |
1770365 |
2.04 % |
| |
|
|
|
|
| Transition |
A>G |
Passed |
1959920 |
24.18 % |
| Transition |
G>A |
Passed |
780045 |
9.62 % |
| Transition |
T>C |
Passed |
1969350 |
24.30 % |
| Transition |
C>T |
Passed |
804226 |
9.92 % |
| Transversion |
A>C |
Passed |
421014 |
5.19 % |
| Transversion |
C>A |
Passed |
256993 |
3.17 % |
| Transversion |
T>G |
Passed |
398580 |
4.92 % |
| Transversion |
G>T |
Passed |
265202 |
3.27 % |
| Transversion |
A>T |
Passed |
300899 |
3.71 % |
| Transversion |
T>A |
Passed |
282776 |
3.49 % |
| Transversion |
C>G |
Passed |
327814 |
4.04 % |
| Transversion |
G>C |
Passed |
338516 |
4.18 % |
| |
|
|
|
|
| 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 |
54685672 |
32299981 |
| Passed |
2.13 |
5513541 |
2591794 |
| dbSNPAll |
0 |
0 |
0 |
| dbSNPPassed |
0 |
0 |
0 |