/CEMT/variants/A95336_2_lane_gembs
BACK
SAMPLE A95336_2_lane_gembs
Variant counts
| Type |
Total |
Pass |
% |
| SNPs |
1164703892 |
1083909740 |
93.06 % |
| Multiallelic |
0 |
0 |
0.00 % |
VCF Filtering Stats
| Type |
#Sites |
% |
#Non-Variant Sites |
% |
#Variant Sites |
% |
| All |
1164703892 |
100% |
1154206273 |
99.10 % |
10497619 |
0.90 % |
| |
|
|
|
|
|
|
| Passed |
1084805458 |
93.14 % |
1081114592 |
93.67 % |
3690866 |
0.34 % |
| Filtered |
79898434 |
6.86 % |
73091681 |
6.33 % |
6806753 |
0.63 % |
| |
|
|
|
|
|
|
| q20 |
53321432 |
66.74 % |
52584343 |
71.94 % |
737089 |
10.83 % |
| q20,mq40 |
9620700 |
12.04 % |
9483808 |
12.98 % |
136892 |
2.01 % |
| q20,qd2 |
7553609 |
9.45 % |
2539497 |
3.47 % |
5014112 |
73.66 % |
| mq40 |
4455250 |
5.58 % |
4143161 |
5.67 % |
312089 |
4.58 % |
| qd2 |
2528161 |
3.16 % |
2167388 |
2.97 % |
360773 |
5.30 % |
| q20,qd2,mq40 |
2297946 |
2.88 % |
2078813 |
2.84 % |
219133 |
3.22 % |
| qd2,mq40 |
113824 |
0.14 % |
94671 |
0.13 % |
19153 |
0.28 % |
| fs60 |
1976 |
0.00 % |
0 |
0.00 % |
1976 |
0.03 % |
| qd2,fs60,mq40 |
1665 |
0.00 % |
0 |
0.00 % |
1665 |
0.02 % |
| q20,qd2,fs60 |
1508 |
0.00 % |
0 |
0.00 % |
1508 |
0.02 % |
| qd2,fs60 |
1343 |
0.00 % |
0 |
0.00 % |
1343 |
0.02 % |
| fs60,mq40 |
722 |
0.00 % |
0 |
0.00 % |
722 |
0.01 % |
| q20,qd2,fs60,mq40 |
287 |
0.00 % |
0 |
0.00 % |
287 |
0.00 % |
| q20,fs60,mq40 |
10 |
0.00 % |
0 |
0.00 % |
10 |
0.00 % |
| q20,fs60 |
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 |
3656899 |
29.74 % |
| Transition |
G>A |
All |
1237699 |
10.07 % |
| Transition |
T>C |
All |
3645912 |
29.66 % |
| Transition |
C>T |
All |
1244125 |
10.12 % |
| Transversion |
A>C |
All |
309141 |
2.51 % |
| Transversion |
C>A |
All |
358318 |
2.91 % |
| Transversion |
T>G |
All |
316786 |
2.58 % |
| Transversion |
G>T |
All |
354306 |
2.88 % |
| Transversion |
A>T |
All |
325988 |
2.65 % |
| Transversion |
T>A |
All |
328238 |
2.67 % |
| Transversion |
C>G |
All |
260554 |
2.12 % |
| Transversion |
G>C |
All |
256250 |
2.08 % |
| |
|
|
|
|
| Transition |
A>G |
Passed |
730909 |
18.00 % |
| Transition |
G>A |
Passed |
629348 |
15.50 % |
| Transition |
T>C |
Passed |
738722 |
18.19 % |
| Transition |
C>T |
Passed |
629089 |
15.49 % |
| Transversion |
A>C |
Passed |
178909 |
4.41 % |
| Transversion |
C>A |
Passed |
177252 |
4.36 % |
| Transversion |
T>G |
Passed |
179780 |
4.43 % |
| Transversion |
G>T |
Passed |
169030 |
4.16 % |
| Transversion |
A>T |
Passed |
141554 |
3.49 % |
| Transversion |
T>A |
Passed |
143674 |
3.54 % |
| Transversion |
C>G |
Passed |
171699 |
4.23 % |
| Transversion |
G>C |
Passed |
171417 |
4.22 % |
| |
|
|
|
|
| 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 |
3.90 |
9784635 |
2509581 |
| Passed |
2.05 |
2728068 |
1333315 |
| dbSNPAll |
0 |
0 |
0 |
| dbSNPPassed |
0 |
0 |
0 |