/cemt/variants/K005739_0_lane_gembs
BACK
SAMPLE K005739_0_lane_gembs
Variant counts
| Type |
Total |
Pass |
% |
| SNPs |
1172225165 |
736361110 |
62.82 % |
| Multiallelic |
0 |
0 |
0.00 % |
VCF Filtering Stats
| Type |
#Sites |
% |
#Non-Variant Sites |
% |
#Variant Sites |
% |
| All |
1172225165 |
100% |
1151715403 |
98.25 % |
20509762 |
1.75 % |
| |
|
|
|
|
|
|
| Passed |
740671049 |
63.19 % |
733575062 |
63.69 % |
7095987 |
0.96 % |
| Filtered |
431554116 |
36.81 % |
418140341 |
36.31 % |
13413775 |
1.81 % |
| |
|
|
|
|
|
|
| q20 |
394042752 |
91.31 % |
390960388 |
93.50 % |
3082364 |
22.98 % |
| q20,qd2 |
19241811 |
4.46 % |
9798620 |
2.34 % |
9443191 |
70.40 % |
| q20,mq40 |
10643890 |
2.47 % |
10510671 |
2.51 % |
133219 |
0.99 % |
| q20,qd2,mq40 |
2727212 |
0.63 % |
2576206 |
0.62 % |
151006 |
1.13 % |
| qd2 |
2634914 |
0.61 % |
2269881 |
0.54 % |
365033 |
2.72 % |
| mq40 |
2221192 |
0.51 % |
1991837 |
0.48 % |
229355 |
1.71 % |
| qd2,mq40 |
40667 |
0.01 % |
32738 |
0.01 % |
7929 |
0.06 % |
| qd2,fs60,mq40 |
751 |
0.00 % |
0 |
0.00 % |
751 |
0.01 % |
| qd2,fs60 |
420 |
0.00 % |
0 |
0.00 % |
420 |
0.00 % |
| fs60,mq40 |
193 |
0.00 % |
0 |
0.00 % |
193 |
0.00 % |
| fs60 |
173 |
0.00 % |
0 |
0.00 % |
173 |
0.00 % |
| q20,qd2,fs60 |
72 |
0.00 % |
0 |
0.00 % |
72 |
0.00 % |
| q20,qd2,fs60,mq40 |
68 |
0.00 % |
0 |
0.00 % |
68 |
0.00 % |
| q20,fs60,mq40 |
1 |
0.00 % |
0 |
0.00 % |
1 |
0.00 % |
| q20,fs60 |
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 |
7940412 |
35.46 % |
| Transition |
G>A |
All |
1037188 |
4.63 % |
| Transition |
T>C |
All |
7115388 |
31.77 % |
| Transition |
C>T |
All |
1098519 |
4.91 % |
| Transversion |
A>C |
All |
532197 |
2.38 % |
| Transversion |
C>A |
All |
1002172 |
4.48 % |
| Transversion |
T>G |
All |
574366 |
2.56 % |
| Transversion |
G>T |
All |
965095 |
4.31 % |
| Transversion |
A>T |
All |
486336 |
2.17 % |
| Transversion |
T>A |
All |
527543 |
2.36 % |
| Transversion |
C>G |
All |
573430 |
2.56 % |
| Transversion |
G>C |
All |
541559 |
2.42 % |
| |
|
|
|
|
| Transition |
A>G |
Passed |
771240 |
20.96 % |
| Transition |
G>A |
Passed |
485588 |
13.20 % |
| Transition |
T>C |
Passed |
781065 |
21.23 % |
| Transition |
C>T |
Passed |
496128 |
13.49 % |
| Transversion |
A>C |
Passed |
140019 |
3.81 % |
| Transversion |
C>A |
Passed |
160050 |
4.35 % |
| Transversion |
T>G |
Passed |
142119 |
3.86 % |
| Transversion |
G>T |
Passed |
155851 |
4.24 % |
| Transversion |
A>T |
Passed |
133542 |
3.63 % |
| Transversion |
T>A |
Passed |
134878 |
3.67 % |
| Transversion |
C>G |
Passed |
139786 |
3.80 % |
| Transversion |
G>C |
Passed |
138648 |
3.77 % |
| |
|
|
|
|
| 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 |
3.30 |
17191507 |
5202698 |
| Passed |
2.21 |
2534021 |
1144893 |
| dbSNPAll |
0 |
0 |
0 |
| dbSNPPassed |
0 |
0 |
0 |