/cemt/variants/A36315_3_lane_gembs
BACK
SAMPLE A36315_3_lane_gembs
Variant counts
| Type |
Total |
Pass |
% |
| SNPs |
1159998089 |
452974619 |
39.05 % |
| Multiallelic |
0 |
0 |
0.00 % |
VCF Filtering Stats
| Type |
#Sites |
% |
#Non-Variant Sites |
% |
#Variant Sites |
% |
| All |
1159998089 |
100% |
1135606798 |
97.90 % |
24391291 |
2.10 % |
| |
|
|
|
|
|
|
| Passed |
457516838 |
39.44 % |
451196601 |
39.73 % |
6320237 |
1.38 % |
| Filtered |
702481251 |
60.56 % |
684410197 |
60.27 % |
18071054 |
3.95 % |
| |
|
|
|
|
|
|
| q20 |
643283189 |
91.57 % |
637733426 |
93.18 % |
5549763 |
30.71 % |
| q20,qd2 |
36713567 |
5.23 % |
24869220 |
3.63 % |
11844347 |
65.54 % |
| q20,mq40 |
11499763 |
1.64 % |
11321505 |
1.65 % |
178258 |
0.99 % |
| qd2 |
6026475 |
0.86 % |
5867687 |
0.86 % |
158788 |
0.88 % |
| q20,qd2,mq40 |
3830994 |
0.55 % |
3652511 |
0.53 % |
178483 |
0.99 % |
| mq40 |
1050343 |
0.15 % |
916232 |
0.13 % |
134111 |
0.74 % |
| qd2,mq40 |
59105 |
0.01 % |
49616 |
0.01 % |
9489 |
0.05 % |
| q20,qd2,fs60 |
5971 |
0.00 % |
0 |
0.00 % |
5971 |
0.03 % |
| fs60 |
5945 |
0.00 % |
0 |
0.00 % |
5945 |
0.03 % |
| qd2,fs60 |
3921 |
0.00 % |
0 |
0.00 % |
3921 |
0.02 % |
| qd2,fs60,mq40 |
1348 |
0.00 % |
0 |
0.00 % |
1348 |
0.01 % |
| fs60,mq40 |
404 |
0.00 % |
0 |
0.00 % |
404 |
0.00 % |
| q20,qd2,fs60,mq40 |
209 |
0.00 % |
0 |
0.00 % |
209 |
0.00 % |
| q20,fs60 |
16 |
0.00 % |
0 |
0.00 % |
16 |
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 |
7028098 |
25.96 % |
| Transition |
G>A |
All |
2045003 |
7.55 % |
| Transition |
T>C |
All |
6423997 |
23.73 % |
| Transition |
C>T |
All |
2042829 |
7.55 % |
| Transversion |
A>C |
All |
542136 |
2.00 % |
| Transversion |
C>A |
All |
1859203 |
6.87 % |
| Transversion |
T>G |
All |
594402 |
2.20 % |
| Transversion |
G>T |
All |
1817880 |
6.72 % |
| Transversion |
A>T |
All |
1877935 |
6.94 % |
| Transversion |
T>A |
All |
1940684 |
7.17 % |
| Transversion |
C>G |
All |
467728 |
1.73 % |
| Transversion |
G>C |
All |
430917 |
1.59 % |
| |
|
|
|
|
| Transition |
A>G |
Passed |
403147 |
17.25 % |
| Transition |
G>A |
Passed |
353239 |
15.11 % |
| Transition |
T>C |
Passed |
395704 |
16.93 % |
| Transition |
C>T |
Passed |
357950 |
15.32 % |
| Transversion |
A>C |
Passed |
97091 |
4.15 % |
| Transversion |
C>A |
Passed |
117491 |
5.03 % |
| Transversion |
T>G |
Passed |
98262 |
4.20 % |
| Transversion |
G>T |
Passed |
114840 |
4.91 % |
| Transversion |
A>T |
Passed |
109042 |
4.67 % |
| Transversion |
T>A |
Passed |
111177 |
4.76 % |
| Transversion |
C>G |
Passed |
89569 |
3.83 % |
| Transversion |
G>C |
Passed |
89601 |
3.83 % |
| |
|
|
|
|
| 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 |
1.84 |
17539927 |
9530885 |
| Passed |
1.83 |
1510040 |
827073 |
| dbSNPAll |
0 |
0 |
0 |
| dbSNPPassed |
0 |
0 |
0 |