/cemt/variants/A63255_3_lane_gembs
BACK
SAMPLE A63255_3_lane_gembs
Variant counts
| Type |
Total |
Pass |
% |
| SNPs |
1163699339 |
733136700 |
63.00 % |
| Multiallelic |
0 |
0 |
0.00 % |
VCF Filtering Stats
| Type |
#Sites |
% |
#Non-Variant Sites |
% |
#Variant Sites |
% |
| All |
1163699339 |
100% |
1146649741 |
98.53 % |
17049598 |
1.47 % |
| |
|
|
|
|
|
|
| Passed |
736585602 |
63.30 % |
730841346 |
63.74 % |
5744256 |
0.78 % |
| Filtered |
427113737 |
36.70 % |
415808395 |
36.26 % |
11305342 |
1.53 % |
| |
|
|
|
|
|
|
| q20 |
387081468 |
90.63 % |
384226692 |
92.40 % |
2854776 |
25.25 % |
| q20,qd2 |
22046964 |
5.16 % |
14373960 |
3.46 % |
7673004 |
67.87 % |
| q20,mq40 |
10842182 |
2.54 % |
10711251 |
2.58 % |
130931 |
1.16 % |
| q20,qd2,mq40 |
2926717 |
0.69 % |
2780552 |
0.67 % |
146165 |
1.29 % |
| mq40 |
2104314 |
0.49 % |
1875648 |
0.45 % |
228666 |
2.02 % |
| qd2 |
2060178 |
0.48 % |
1799346 |
0.43 % |
260832 |
2.31 % |
| qd2,mq40 |
49282 |
0.01 % |
40946 |
0.01 % |
8336 |
0.07 % |
| qd2,fs60,mq40 |
949 |
0.00 % |
0 |
0.00 % |
949 |
0.01 % |
| qd2,fs60 |
611 |
0.00 % |
0 |
0.00 % |
611 |
0.01 % |
| fs60 |
386 |
0.00 % |
0 |
0.00 % |
386 |
0.00 % |
| q20,qd2,fs60 |
293 |
0.00 % |
0 |
0.00 % |
293 |
0.00 % |
| fs60,mq40 |
240 |
0.00 % |
0 |
0.00 % |
240 |
0.00 % |
| q20,qd2,fs60,mq40 |
153 |
0.00 % |
0 |
0.00 % |
153 |
0.00 % |
| q20,fs60 |
0 |
0.00 % |
0 |
0.00 % |
0 |
0.00 % |
| q20,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 |
6698042 |
35.29 % |
| Transition |
G>A |
All |
862324 |
4.54 % |
| Transition |
T>C |
All |
6735905 |
35.48 % |
| Transition |
C>T |
All |
872831 |
4.60 % |
| Transversion |
A>C |
All |
548855 |
2.89 % |
| Transversion |
C>A |
All |
481520 |
2.54 % |
| Transversion |
T>G |
All |
549323 |
2.89 % |
| Transversion |
G>T |
All |
473709 |
2.50 % |
| Transversion |
A>T |
All |
434649 |
2.29 % |
| Transversion |
T>A |
All |
443021 |
2.33 % |
| Transversion |
C>G |
All |
440416 |
2.32 % |
| Transversion |
G>C |
All |
441827 |
2.33 % |
| |
|
|
|
|
| Transition |
A>G |
Passed |
654236 |
20.55 % |
| Transition |
G>A |
Passed |
454675 |
14.28 % |
| Transition |
T>C |
Passed |
611708 |
19.21 % |
| Transition |
C>T |
Passed |
456330 |
14.33 % |
| Transversion |
A>C |
Passed |
131736 |
4.14 % |
| Transversion |
C>A |
Passed |
132296 |
4.15 % |
| Transversion |
T>G |
Passed |
132005 |
4.15 % |
| Transversion |
G>T |
Passed |
127369 |
4.00 % |
| Transversion |
A>T |
Passed |
119301 |
3.75 % |
| Transversion |
T>A |
Passed |
120698 |
3.79 % |
| Transversion |
C>G |
Passed |
121526 |
3.82 % |
| Transversion |
G>C |
Passed |
122264 |
3.84 % |
| |
|
|
|
|
| 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 |
3.98 |
15169102 |
3813320 |
| Passed |
2.16 |
2176949 |
1007195 |
| dbSNPAll |
0 |
0 |
0 |
| dbSNPPassed |
0 |
0 |
0 |