/cemt/variants/K005727_0_lane_gembs
BACK
SAMPLE K005727_0_lane_gembs
Variant counts
| Type |
Total |
Pass |
% |
| SNPs |
1168712770 |
704723563 |
60.30 % |
| Multiallelic |
0 |
0 |
0.00 % |
VCF Filtering Stats
| Type |
#Sites |
% |
#Non-Variant Sites |
% |
#Variant Sites |
% |
| All |
1168712770 |
100% |
1145218885 |
97.99 % |
23493885 |
2.01 % |
| |
|
|
|
|
|
|
| Passed |
709619119 |
60.72 % |
701651041 |
61.27 % |
7968078 |
1.12 % |
| Filtered |
459093651 |
39.28 % |
443567844 |
38.73 % |
15525807 |
2.19 % |
| |
|
|
|
|
|
|
| q20 |
418441125 |
91.15 % |
415350736 |
93.64 % |
3090389 |
19.90 % |
| q20,qd2 |
21364663 |
4.65 % |
9968250 |
2.25 % |
11396413 |
73.40 % |
| q20,mq40 |
11144024 |
2.43 % |
10996799 |
2.48 % |
147225 |
0.95 % |
| qd2 |
2908338 |
0.63 % |
2489805 |
0.56 % |
418533 |
2.70 % |
| q20,qd2,mq40 |
2869391 |
0.63 % |
2689139 |
0.61 % |
180252 |
1.16 % |
| mq40 |
2316543 |
0.50 % |
2034961 |
0.46 % |
281582 |
1.81 % |
| qd2,mq40 |
48192 |
0.01 % |
38154 |
0.01 % |
10038 |
0.06 % |
| qd2,fs60,mq40 |
580 |
0.00 % |
0 |
0.00 % |
580 |
0.00 % |
| qd2,fs60 |
317 |
0.00 % |
0 |
0.00 % |
317 |
0.00 % |
| fs60,mq40 |
243 |
0.00 % |
0 |
0.00 % |
243 |
0.00 % |
| fs60 |
139 |
0.00 % |
0 |
0.00 % |
139 |
0.00 % |
| q20,qd2,fs60,mq40 |
60 |
0.00 % |
0 |
0.00 % |
60 |
0.00 % |
| q20,qd2,fs60 |
35 |
0.00 % |
0 |
0.00 % |
35 |
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 |
8985166 |
35.35 % |
| Transition |
G>A |
All |
1261678 |
4.96 % |
| Transition |
T>C |
All |
8082005 |
31.79 % |
| Transition |
C>T |
All |
1272416 |
5.01 % |
| Transversion |
A>C |
All |
452693 |
1.78 % |
| Transversion |
C>A |
All |
1215049 |
4.78 % |
| Transversion |
T>G |
All |
516899 |
2.03 % |
| Transversion |
G>T |
All |
1159198 |
4.56 % |
| Transversion |
A>T |
All |
643762 |
2.53 % |
| Transversion |
T>A |
All |
691798 |
2.72 % |
| Transversion |
C>G |
All |
600202 |
2.36 % |
| Transversion |
G>C |
All |
539078 |
2.12 % |
| |
|
|
|
|
| Transition |
A>G |
Passed |
918943 |
23.54 % |
| Transition |
G>A |
Passed |
492297 |
12.61 % |
| Transition |
T>C |
Passed |
815639 |
20.89 % |
| Transition |
C>T |
Passed |
494243 |
12.66 % |
| Transversion |
A>C |
Passed |
142357 |
3.65 % |
| Transversion |
C>A |
Passed |
167642 |
4.29 % |
| Transversion |
T>G |
Passed |
146179 |
3.74 % |
| Transversion |
G>T |
Passed |
157526 |
4.03 % |
| Transversion |
A>T |
Passed |
136549 |
3.50 % |
| Transversion |
T>A |
Passed |
139901 |
3.58 % |
| Transversion |
C>G |
Passed |
148242 |
3.80 % |
| Transversion |
G>C |
Passed |
144857 |
3.71 % |
| |
|
|
|
|
| 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 |
3.37 |
19601265 |
5818679 |
| Passed |
2.30 |
2721122 |
1183253 |
| dbSNPAll |
0 |
0 |
0 |
| dbSNPPassed |
0 |
0 |
0 |