/cemt/variants/A54769_3_lane_gembs
BACK
SAMPLE A54769_3_lane_gembs
Variant counts
| Type |
Total |
Pass |
% |
| SNPs |
1159021237 |
585551292 |
50.52 % |
| Multiallelic |
0 |
0 |
0.00 % |
VCF Filtering Stats
| Type |
#Sites |
% |
#Non-Variant Sites |
% |
#Variant Sites |
% |
| All |
1159021237 |
100% |
1135099675 |
97.94 % |
23921562 |
2.06 % |
| |
|
|
|
|
|
|
| Passed |
589657343 |
50.88 % |
583479024 |
51.40 % |
6178319 |
1.05 % |
| Filtered |
569363894 |
49.12 % |
551620651 |
48.60 % |
17743243 |
3.01 % |
| |
|
|
|
|
|
|
| q20 |
508600861 |
89.33 % |
503538281 |
91.28 % |
5062580 |
28.53 % |
| q20,qd2 |
29375229 |
5.16 % |
17532270 |
3.18 % |
11842959 |
66.75 % |
| qd2 |
14739897 |
2.59 % |
14511193 |
2.63 % |
228704 |
1.29 % |
| q20,mq40 |
11447924 |
2.01 % |
11252662 |
2.04 % |
195262 |
1.10 % |
| q20,qd2,mq40 |
3527527 |
0.62 % |
3314839 |
0.60 % |
212688 |
1.20 % |
| mq40 |
1568120 |
0.28 % |
1405296 |
0.25 % |
162824 |
0.92 % |
| qd2,mq40 |
78482 |
0.01 % |
66110 |
0.01 % |
12372 |
0.07 % |
| q20,qd2,fs60 |
8754 |
0.00 % |
0 |
0.00 % |
8754 |
0.05 % |
| qd2,fs60 |
7242 |
0.00 % |
0 |
0.00 % |
7242 |
0.04 % |
| fs60 |
7069 |
0.00 % |
0 |
0.00 % |
7069 |
0.04 % |
| qd2,fs60,mq40 |
1897 |
0.00 % |
0 |
0.00 % |
1897 |
0.01 % |
| fs60,mq40 |
541 |
0.00 % |
0 |
0.00 % |
541 |
0.00 % |
| q20,qd2,fs60,mq40 |
337 |
0.00 % |
0 |
0.00 % |
337 |
0.00 % |
| q20,fs60 |
12 |
0.00 % |
0 |
0.00 % |
12 |
0.00 % |
| q20,fs60,mq40 |
2 |
0.00 % |
0 |
0.00 % |
2 |
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 |
7997741 |
29.65 % |
| Transition |
G>A |
All |
2390122 |
8.86 % |
| Transition |
T>C |
All |
6523663 |
24.19 % |
| Transition |
C>T |
All |
2434699 |
9.03 % |
| Transversion |
A>C |
All |
437699 |
1.62 % |
| Transversion |
C>A |
All |
1578759 |
5.85 % |
| Transversion |
T>G |
All |
533893 |
1.98 % |
| Transversion |
G>T |
All |
1493370 |
5.54 % |
| Transversion |
A>T |
All |
1328673 |
4.93 % |
| Transversion |
T>A |
All |
1412033 |
5.24 % |
| Transversion |
C>G |
All |
457254 |
1.70 % |
| Transversion |
G>C |
All |
381830 |
1.42 % |
| |
|
|
|
|
| Transition |
A>G |
Passed |
527730 |
19.04 % |
| Transition |
G>A |
Passed |
413183 |
14.91 % |
| Transition |
T>C |
Passed |
490465 |
17.70 % |
| Transition |
C>T |
Passed |
416177 |
15.02 % |
| Transversion |
A>C |
Passed |
111516 |
4.02 % |
| Transversion |
C>A |
Passed |
128444 |
4.63 % |
| Transversion |
T>G |
Passed |
114437 |
4.13 % |
| Transversion |
G>T |
Passed |
125670 |
4.53 % |
| Transversion |
A>T |
Passed |
113382 |
4.09 % |
| Transversion |
T>A |
Passed |
116975 |
4.22 % |
| Transversion |
C>G |
Passed |
107110 |
3.86 % |
| Transversion |
G>C |
Passed |
106541 |
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 |
2.54 |
19346225 |
7623511 |
| Passed |
2.00 |
1847555 |
924075 |
| dbSNPAll |
0 |
0 |
0 |
| dbSNPPassed |
0 |
0 |
0 |