/cemt/variants/A56420_3_lane_gembs
BACK
SAMPLE A56420_3_lane_gembs
Variant counts
| Type |
Total |
Pass |
% |
| SNPs |
1173600494 |
790550521 |
67.36 % |
| Multiallelic |
0 |
0 |
0.00 % |
VCF Filtering Stats
| Type |
#Sites |
% |
#Non-Variant Sites |
% |
#Variant Sites |
% |
| All |
1173600494 |
100% |
1154958591 |
98.41 % |
18641903 |
1.59 % |
| |
|
|
|
|
|
|
| Passed |
794190591 |
67.67 % |
788037747 |
68.23 % |
6152844 |
0.77 % |
| Filtered |
379409903 |
32.33 % |
366920844 |
31.77 % |
12489059 |
1.57 % |
| |
|
|
|
|
|
|
| q20 |
345852840 |
91.16 % |
342883732 |
93.45 % |
2969108 |
23.77 % |
| q20,qd2 |
15634595 |
4.12 % |
6912315 |
1.88 % |
8722280 |
69.84 % |
| q20,mq40 |
11238470 |
2.96 % |
11098876 |
3.02 % |
139594 |
1.12 % |
| q20,qd2,mq40 |
2738545 |
0.72 % |
2594256 |
0.71 % |
144289 |
1.16 % |
| mq40 |
2173948 |
0.57 % |
1939045 |
0.53 % |
234903 |
1.88 % |
| qd2 |
1719275 |
0.45 % |
1451326 |
0.40 % |
267949 |
2.15 % |
| qd2,mq40 |
49863 |
0.01 % |
41294 |
0.01 % |
8569 |
0.07 % |
| qd2,fs60,mq40 |
932 |
0.00 % |
0 |
0.00 % |
932 |
0.01 % |
| qd2,fs60 |
527 |
0.00 % |
0 |
0.00 % |
527 |
0.00 % |
| fs60 |
316 |
0.00 % |
0 |
0.00 % |
316 |
0.00 % |
| fs60,mq40 |
311 |
0.00 % |
0 |
0.00 % |
311 |
0.00 % |
| q20,qd2,fs60 |
171 |
0.00 % |
0 |
0.00 % |
171 |
0.00 % |
| q20,qd2,fs60,mq40 |
109 |
0.00 % |
0 |
0.00 % |
109 |
0.00 % |
| q20,fs60 |
1 |
0.00 % |
0 |
0.00 % |
1 |
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 |
7442158 |
36.31 % |
| Transition |
G>A |
All |
862748 |
4.21 % |
| Transition |
T>C |
All |
7510912 |
36.65 % |
| Transition |
C>T |
All |
869837 |
4.24 % |
| Transversion |
A>C |
All |
608854 |
2.97 % |
| Transversion |
C>A |
All |
438348 |
2.14 % |
| Transversion |
T>G |
All |
603679 |
2.95 % |
| Transversion |
G>T |
All |
429328 |
2.09 % |
| Transversion |
A>T |
All |
418855 |
2.04 % |
| Transversion |
T>A |
All |
425444 |
2.08 % |
| Transversion |
C>G |
All |
441478 |
2.15 % |
| Transversion |
G>C |
All |
442339 |
2.16 % |
| |
|
|
|
|
| Transition |
A>G |
Passed |
702572 |
20.35 % |
| Transition |
G>A |
Passed |
481772 |
13.96 % |
| Transition |
T>C |
Passed |
688454 |
19.94 % |
| Transition |
C>T |
Passed |
484283 |
14.03 % |
| Transversion |
A>C |
Passed |
146826 |
4.25 % |
| Transversion |
C>A |
Passed |
142560 |
4.13 % |
| Transversion |
T>G |
Passed |
146558 |
4.25 % |
| Transversion |
G>T |
Passed |
137942 |
4.00 % |
| Transversion |
A>T |
Passed |
125025 |
3.62 % |
| Transversion |
T>A |
Passed |
125919 |
3.65 % |
| Transversion |
C>G |
Passed |
135196 |
3.92 % |
| Transversion |
G>C |
Passed |
135216 |
3.92 % |
| |
|
|
|
|
| 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 |
4.38 |
16685655 |
3808325 |
| Passed |
2.15 |
2357081 |
1095242 |
| dbSNPAll |
0 |
0 |
0 |
| dbSNPPassed |
0 |
0 |
0 |