/CEMT/variants/A95337_2_lane_gembs
BACK
SAMPLE A95337_2_lane_gembs
Variant counts
| Type |
Total |
Pass |
% |
| SNPs |
1165116091 |
1087835816 |
93.37 % |
| Multiallelic |
0 |
0 |
0.00 % |
VCF Filtering Stats
| Type |
#Sites |
% |
#Non-Variant Sites |
% |
#Variant Sites |
% |
| All |
1165116091 |
100% |
1154668226 |
99.10 % |
10447865 |
0.90 % |
| |
|
|
|
|
|
|
| Passed |
1088680197 |
93.44 % |
1084964319 |
93.96 % |
3715878 |
0.34 % |
| Filtered |
76435894 |
6.56 % |
69703907 |
6.04 % |
6731987 |
0.62 % |
| |
|
|
|
|
|
|
| q20 |
49951421 |
65.35 % |
49267145 |
70.68 % |
684276 |
10.16 % |
| q20,mq40 |
9944777 |
13.01 % |
9798270 |
14.06 % |
146507 |
2.18 % |
| q20,qd2 |
7135357 |
9.34 % |
2169350 |
3.11 % |
4966007 |
73.77 % |
| mq40 |
4277526 |
5.60 % |
3959051 |
5.68 % |
318475 |
4.73 % |
| qd2 |
2611513 |
3.42 % |
2242444 |
3.22 % |
369069 |
5.48 % |
| q20,qd2,mq40 |
2401103 |
3.14 % |
2178859 |
3.13 % |
222244 |
3.30 % |
| qd2,mq40 |
107316 |
0.14 % |
88788 |
0.13 % |
18528 |
0.28 % |
| fs60 |
1848 |
0.00 % |
0 |
0.00 % |
1848 |
0.03 % |
| qd2,fs60,mq40 |
1553 |
0.00 % |
0 |
0.00 % |
1553 |
0.02 % |
| qd2,fs60 |
1295 |
0.00 % |
0 |
0.00 % |
1295 |
0.02 % |
| q20,qd2,fs60 |
1268 |
0.00 % |
0 |
0.00 % |
1268 |
0.02 % |
| fs60,mq40 |
669 |
0.00 % |
0 |
0.00 % |
669 |
0.01 % |
| q20,qd2,fs60,mq40 |
239 |
0.00 % |
0 |
0.00 % |
239 |
0.00 % |
| q20,fs60,mq40 |
8 |
0.00 % |
0 |
0.00 % |
8 |
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 |
3801166 |
31.11 % |
| Transition |
G>A |
All |
1029266 |
8.42 % |
| Transition |
T>C |
All |
3785143 |
30.98 % |
| Transition |
C>T |
All |
1035115 |
8.47 % |
| Transversion |
A>C |
All |
324297 |
2.65 % |
| Transversion |
C>A |
All |
357708 |
2.93 % |
| Transversion |
T>G |
All |
331082 |
2.71 % |
| Transversion |
G>T |
All |
354223 |
2.90 % |
| Transversion |
A>T |
All |
327349 |
2.68 % |
| Transversion |
T>A |
All |
330306 |
2.70 % |
| Transversion |
C>G |
All |
274021 |
2.24 % |
| Transversion |
G>C |
All |
270179 |
2.21 % |
| |
|
|
|
|
| Transition |
A>G |
Passed |
750240 |
18.08 % |
| Transition |
G>A |
Passed |
636524 |
15.34 % |
| Transition |
T>C |
Passed |
758091 |
18.27 % |
| Transition |
C>T |
Passed |
636617 |
15.34 % |
| Transversion |
A>C |
Passed |
183944 |
4.43 % |
| Transversion |
C>A |
Passed |
182865 |
4.41 % |
| Transversion |
T>G |
Passed |
184655 |
4.45 % |
| Transversion |
G>T |
Passed |
174230 |
4.20 % |
| Transversion |
A>T |
Passed |
147192 |
3.55 % |
| Transversion |
T>A |
Passed |
149201 |
3.59 % |
| Transversion |
C>G |
Passed |
173535 |
4.18 % |
| Transversion |
G>C |
Passed |
173283 |
4.18 % |
| |
|
|
|
|
| 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 |
3.76 |
9650690 |
2569165 |
| Passed |
2.03 |
2781472 |
1368905 |
| dbSNPAll |
0 |
0 |
0 |
| dbSNPPassed |
0 |
0 |
0 |