/Martin Hirst/variants/PX0720_AAGCGA_10_lane_gembs
BACK
SAMPLE PX0720_AAGCGA_10_lane_gembs
Variant counts
| Type |
Total |
Pass |
% |
| SNPs |
1200008833 |
600185826 |
50.02 % |
| Multiallelic |
0 |
0 |
0.00 % |
VCF Filtering Stats
| Type |
#Sites |
% |
#Non-Variant Sites |
% |
#Variant Sites |
% |
| All |
1200008833 |
100% |
1113479726 |
92.79 % |
86529107 |
7.21 % |
| |
|
|
|
|
|
|
| Passed |
621894109 |
51.82 % |
594894060 |
53.43 % |
27000049 |
4.34 % |
| Filtered |
578114724 |
48.18 % |
518585666 |
46.57 % |
59529058 |
9.57 % |
| |
|
|
|
|
|
|
| q20 |
473513261 |
81.91 % |
454018750 |
87.55 % |
19494511 |
32.75 % |
| q20,qd2 |
77282418 |
13.37 % |
38801307 |
7.48 % |
38481111 |
64.64 % |
| qd2 |
12360345 |
2.14 % |
11464560 |
2.21 % |
895785 |
1.50 % |
| q20,mq40 |
9559432 |
1.65 % |
9331867 |
1.80 % |
227565 |
0.38 % |
| q20,qd2,mq40 |
4736888 |
0.82 % |
4573923 |
0.88 % |
162965 |
0.27 % |
| mq40 |
634758 |
0.11 % |
374137 |
0.07 % |
260621 |
0.44 % |
| qd2,mq40 |
27615 |
0.00 % |
21122 |
0.00 % |
6493 |
0.01 % |
| qd2,fs60 |
5 |
0.00 % |
0 |
0.00 % |
5 |
0.00 % |
| qd2,fs60,mq40 |
2 |
0.00 % |
0 |
0.00 % |
2 |
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 % |
| fs60,mq40 |
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 |
21661890 |
24.10 % |
| Transition |
G>A |
All |
4569566 |
5.08 % |
| Transition |
T>C |
All |
21809983 |
24.26 % |
| Transition |
C>T |
All |
4644386 |
5.17 % |
| Transversion |
A>C |
All |
3723560 |
4.14 % |
| Transversion |
C>A |
All |
4352964 |
4.84 % |
| Transversion |
T>G |
All |
3603013 |
4.01 % |
| Transversion |
G>T |
All |
4446181 |
4.95 % |
| Transversion |
A>T |
All |
8493528 |
9.45 % |
| Transversion |
T>A |
All |
8374440 |
9.32 % |
| Transversion |
C>G |
All |
2067889 |
2.30 % |
| Transversion |
G>C |
All |
2136491 |
2.38 % |
| |
|
|
|
|
| Transition |
A>G |
Passed |
1471641 |
25.65 % |
| Transition |
G>A |
Passed |
472175 |
8.23 % |
| Transition |
T>C |
Passed |
1558965 |
27.17 % |
| Transition |
C>T |
Passed |
485412 |
8.46 % |
| Transversion |
A>C |
Passed |
301714 |
5.26 % |
| Transversion |
C>A |
Passed |
157576 |
2.75 % |
| Transversion |
T>G |
Passed |
283094 |
4.93 % |
| Transversion |
G>T |
Passed |
164144 |
2.86 % |
| Transversion |
A>T |
Passed |
194590 |
3.39 % |
| Transversion |
T>A |
Passed |
182909 |
3.19 % |
| Transversion |
C>G |
Passed |
226570 |
3.95 % |
| Transversion |
G>C |
Passed |
238491 |
4.16 % |
| |
|
|
|
|
| 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 |
1.42 |
52685825 |
37198066 |
| Passed |
2.28 |
3988193 |
1749088 |
| dbSNPAll |
0 |
0 |
0 |
| dbSNPPassed |
0 |
0 |
0 |