/CEMT/variants/B33200_1_lane_gembs
BACK
SAMPLE B33200_1_lane_gembs
Variant counts
| Type |
Total |
Pass |
% |
| SNPs |
1168488359 |
709869718 |
60.75 % |
| Multiallelic |
0 |
0 |
0.00 % |
VCF Filtering Stats
| Type |
#Sites |
% |
#Non-Variant Sites |
% |
#Variant Sites |
% |
| All |
1168488359 |
100% |
1147944974 |
98.24 % |
20543385 |
1.76 % |
| |
|
|
|
|
|
|
| Passed |
715157909 |
61.20 % |
707450573 |
61.63 % |
7707336 |
1.08 % |
| Filtered |
453330450 |
38.80 % |
440494401 |
38.37 % |
12836049 |
1.79 % |
| |
|
|
|
|
|
|
| q20 |
417073842 |
92.00 % |
414724684 |
94.15 % |
2349158 |
18.30 % |
| q20,qd2 |
17119929 |
3.78 % |
7228240 |
1.64 % |
9891689 |
77.06 % |
| q20,mq40 |
9183233 |
2.03 % |
9091595 |
2.06 % |
91638 |
0.71 % |
| qd2 |
5916573 |
1.31 % |
5717007 |
1.30 % |
199566 |
1.55 % |
| q20,qd2,mq40 |
2536686 |
0.56 % |
2434412 |
0.55 % |
102274 |
0.80 % |
| mq40 |
1440783 |
0.32 % |
1259060 |
0.29 % |
181723 |
1.42 % |
| qd2,mq40 |
47683 |
0.01 % |
39403 |
0.01 % |
8280 |
0.06 % |
| fs60 |
4250 |
0.00 % |
0 |
0.00 % |
4250 |
0.03 % |
| qd2,fs60 |
3205 |
0.00 % |
0 |
0.00 % |
3205 |
0.02 % |
| q20,qd2,fs60 |
2418 |
0.00 % |
0 |
0.00 % |
2418 |
0.02 % |
| qd2,fs60,mq40 |
1364 |
0.00 % |
0 |
0.00 % |
1364 |
0.01 % |
| fs60,mq40 |
312 |
0.00 % |
0 |
0.00 % |
312 |
0.00 % |
| q20,qd2,fs60,mq40 |
159 |
0.00 % |
0 |
0.00 % |
159 |
0.00 % |
| q20,fs60 |
12 |
0.00 % |
0 |
0.00 % |
12 |
0.00 % |
| q20,fs60,mq40 |
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 |
8090116 |
36.05 % |
| Transition |
G>A |
All |
1114974 |
4.97 % |
| Transition |
T>C |
All |
8090252 |
36.05 % |
| Transition |
C>T |
All |
1113418 |
4.96 % |
| Transversion |
A>C |
All |
490823 |
2.19 % |
| Transversion |
C>A |
All |
681525 |
3.04 % |
| Transversion |
T>G |
All |
490882 |
2.19 % |
| Transversion |
G>T |
All |
679704 |
3.03 % |
| Transversion |
A>T |
All |
422162 |
1.88 % |
| Transversion |
T>A |
All |
424281 |
1.89 % |
| Transversion |
C>G |
All |
421769 |
1.88 % |
| Transversion |
G>C |
All |
421786 |
1.88 % |
| |
|
|
|
|
| Transition |
A>G |
Passed |
639309 |
19.60 % |
| Transition |
G>A |
Passed |
464302 |
14.23 % |
| Transition |
T>C |
Passed |
628113 |
19.25 % |
| Transition |
C>T |
Passed |
464518 |
14.24 % |
| Transversion |
A>C |
Passed |
140323 |
4.30 % |
| Transversion |
C>A |
Passed |
142219 |
4.36 % |
| Transversion |
T>G |
Passed |
140178 |
4.30 % |
| Transversion |
G>T |
Passed |
137534 |
4.22 % |
| Transversion |
A>T |
Passed |
119920 |
3.68 % |
| Transversion |
T>A |
Passed |
121323 |
3.72 % |
| Transversion |
C>G |
Passed |
132285 |
4.05 % |
| Transversion |
G>C |
Passed |
132404 |
4.06 % |
| |
|
|
|
|
| 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 |
4.56 |
18408760 |
4032932 |
| Passed |
2.06 |
2196242 |
1066186 |
| dbSNPAll |
0 |
0 |
0 |
| dbSNPPassed |
0 |
0 |
0 |