/cemt/variants/A77950_1_lane_gembs
BACK
SAMPLE A77950_1_lane_gembs
Variant counts
| Type |
Total |
Pass |
% |
| SNPs |
1170820765 |
907168671 |
77.48 % |
| Multiallelic |
0 |
0 |
0.00 % |
VCF Filtering Stats
| Type |
#Sites |
% |
#Non-Variant Sites |
% |
#Variant Sites |
% |
| All |
1170820765 |
100% |
1149863157 |
98.21 % |
20957608 |
1.79 % |
| |
|
|
|
|
|
|
| Passed |
910882649 |
77.80 % |
903934552 |
78.61 % |
6948097 |
0.76 % |
| Filtered |
259938116 |
22.20 % |
245928605 |
21.39 % |
14009511 |
1.54 % |
| |
|
|
|
|
|
|
| q20 |
224150052 |
86.23 % |
222622835 |
90.52 % |
1527217 |
10.90 % |
| q20,qd2 |
17027338 |
6.55 % |
5493279 |
2.23 % |
11534059 |
82.33 % |
| q20,mq40 |
11086781 |
4.27 % |
10958305 |
4.46 % |
128476 |
0.92 % |
| q20,qd2,mq40 |
2920817 |
1.12 % |
2761715 |
1.12 % |
159102 |
1.14 % |
| qd2 |
2596384 |
1.00 % |
2211281 |
0.90 % |
385103 |
2.75 % |
| mq40 |
2106205 |
0.81 % |
1841290 |
0.75 % |
264915 |
1.89 % |
| qd2,mq40 |
48906 |
0.02 % |
39900 |
0.02 % |
9006 |
0.06 % |
| qd2,fs60,mq40 |
724 |
0.00 % |
0 |
0.00 % |
724 |
0.01 % |
| qd2,fs60 |
297 |
0.00 % |
0 |
0.00 % |
297 |
0.00 % |
| fs60,mq40 |
240 |
0.00 % |
0 |
0.00 % |
240 |
0.00 % |
| fs60 |
209 |
0.00 % |
0 |
0.00 % |
209 |
0.00 % |
| q20,qd2,fs60 |
94 |
0.00 % |
0 |
0.00 % |
94 |
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 |
8204974 |
36.15 % |
| Transition |
G>A |
All |
1006068 |
4.43 % |
| Transition |
T>C |
All |
8171555 |
36.00 % |
| Transition |
C>T |
All |
1005819 |
4.43 % |
| Transversion |
A>C |
All |
363185 |
1.60 % |
| Transversion |
C>A |
All |
1029447 |
4.54 % |
| Transversion |
T>G |
All |
362949 |
1.60 % |
| Transversion |
G>T |
All |
853391 |
3.76 % |
| Transversion |
A>T |
All |
502667 |
2.21 % |
| Transversion |
T>A |
All |
521421 |
2.30 % |
| Transversion |
C>G |
All |
341535 |
1.50 % |
| Transversion |
G>C |
All |
336344 |
1.48 % |
| |
|
|
|
|
| Transition |
A>G |
Passed |
829842 |
19.38 % |
| Transition |
G>A |
Passed |
556806 |
13.00 % |
| Transition |
T>C |
Passed |
800350 |
18.69 % |
| Transition |
C>T |
Passed |
557204 |
13.01 % |
| Transversion |
A>C |
Passed |
161343 |
3.77 % |
| Transversion |
C>A |
Passed |
330945 |
7.73 % |
| Transversion |
T>G |
Passed |
162600 |
3.80 % |
| Transversion |
G>T |
Passed |
263948 |
6.16 % |
| Transversion |
A>T |
Passed |
152458 |
3.56 % |
| Transversion |
T>A |
Passed |
158947 |
3.71 % |
| Transversion |
C>G |
Passed |
154539 |
3.61 % |
| Transversion |
G>C |
Passed |
153732 |
3.59 % |
| |
|
|
|
|
| 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 |
4.27 |
18388416 |
4310939 |
| Passed |
1.78 |
2744202 |
1538512 |
| dbSNPAll |
0 |
0 |
0 |
| dbSNPPassed |
0 |
0 |
0 |