/cemt/variants/A34042_3_lane_gembs
BACK
SAMPLE A34042_3_lane_gembs
Variant counts
| Type |
Total |
Pass |
% |
| SNPs |
1169866312 |
807215091 |
69.00 % |
| Multiallelic |
0 |
0 |
0.00 % |
VCF Filtering Stats
| Type |
#Sites |
% |
#Non-Variant Sites |
% |
#Variant Sites |
% |
| All |
1169866312 |
100% |
1147786493 |
98.11 % |
22079819 |
1.89 % |
| |
|
|
|
|
|
|
| Passed |
809721461 |
69.21 % |
802862085 |
69.95 % |
6859376 |
0.85 % |
| Filtered |
360144851 |
30.79 % |
344924408 |
30.05 % |
15220443 |
1.88 % |
| |
|
|
|
|
|
|
| q20 |
312863862 |
86.87 % |
309422145 |
89.71 % |
3441717 |
22.61 % |
| q20,qd2 |
22077161 |
6.13 % |
11572557 |
3.36 % |
10504604 |
69.02 % |
| q20,mq40 |
12081149 |
3.35 % |
11824252 |
3.43 % |
256897 |
1.69 % |
| qd2 |
7501909 |
2.08 % |
6995981 |
2.03 % |
505928 |
3.32 % |
| q20,qd2,mq40 |
3263874 |
0.91 % |
2979779 |
0.86 % |
284095 |
1.87 % |
| mq40 |
2275926 |
0.63 % |
2068850 |
0.60 % |
207076 |
1.36 % |
| qd2,mq40 |
71773 |
0.02 % |
60844 |
0.02 % |
10929 |
0.07 % |
| q20,qd2,fs60 |
2787 |
0.00 % |
0 |
0.00 % |
2787 |
0.02 % |
| fs60 |
2648 |
0.00 % |
0 |
0.00 % |
2648 |
0.02 % |
| qd2,fs60 |
1982 |
0.00 % |
0 |
0.00 % |
1982 |
0.01 % |
| qd2,fs60,mq40 |
1324 |
0.00 % |
0 |
0.00 % |
1324 |
0.01 % |
| fs60,mq40 |
334 |
0.00 % |
0 |
0.00 % |
334 |
0.00 % |
| q20,qd2,fs60,mq40 |
118 |
0.00 % |
0 |
0.00 % |
118 |
0.00 % |
| q20,fs60 |
3 |
0.00 % |
0 |
0.00 % |
3 |
0.00 % |
| q20,fs60,mq40 |
1 |
0.00 % |
0 |
0.00 % |
1 |
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 |
6309007 |
27.10 % |
| Transition |
G>A |
All |
2191692 |
9.42 % |
| Transition |
T>C |
All |
6129579 |
26.33 % |
| Transition |
C>T |
All |
2188139 |
9.40 % |
| Transversion |
A>C |
All |
495339 |
2.13 % |
| Transversion |
C>A |
All |
1087416 |
4.67 % |
| Transversion |
T>G |
All |
506880 |
2.18 % |
| Transversion |
G>T |
All |
1081475 |
4.65 % |
| Transversion |
A>T |
All |
1206427 |
5.18 % |
| Transversion |
T>A |
All |
1223921 |
5.26 % |
| Transversion |
C>G |
All |
433275 |
1.86 % |
| Transversion |
G>C |
All |
424213 |
1.82 % |
| |
|
|
|
|
| Transition |
A>G |
Passed |
809428 |
17.45 % |
| Transition |
G>A |
Passed |
715492 |
15.42 % |
| Transition |
T>C |
Passed |
810431 |
17.47 % |
| Transition |
C>T |
Passed |
719767 |
15.52 % |
| Transversion |
A>C |
Passed |
193794 |
4.18 % |
| Transversion |
C>A |
Passed |
216174 |
4.66 % |
| Transversion |
T>G |
Passed |
193648 |
4.17 % |
| Transversion |
G>T |
Passed |
215524 |
4.65 % |
| Transversion |
A>T |
Passed |
189470 |
4.08 % |
| Transversion |
T>A |
Passed |
191787 |
4.13 % |
| Transversion |
C>G |
Passed |
191813 |
4.13 % |
| Transversion |
G>C |
Passed |
191555 |
4.13 % |
| |
|
|
|
|
| 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 |
2.60 |
16818417 |
6458946 |
| Passed |
1.93 |
3055118 |
1583765 |
| dbSNPAll |
0 |
0 |
0 |
| dbSNPPassed |
0 |
0 |
0 |