/cemt/variants/A54764_3_lane_gembs
BACK
SAMPLE A54764_3_lane_gembs
Variant counts
| Type |
Total |
Pass |
% |
| SNPs |
1168002721 |
529863988 |
45.36 % |
| Multiallelic |
0 |
0 |
0.00 % |
VCF Filtering Stats
| Type |
#Sites |
% |
#Non-Variant Sites |
% |
#Variant Sites |
% |
| All |
1168002721 |
100% |
1137881559 |
97.42 % |
30121162 |
2.58 % |
| |
|
|
|
|
|
|
| Passed |
534459626 |
45.76 % |
527826425 |
46.39 % |
6633201 |
1.24 % |
| Filtered |
633543095 |
54.24 % |
610055134 |
53.61 % |
23487961 |
4.39 % |
| |
|
|
|
|
|
|
| q20 |
563880620 |
89.00 % |
556128974 |
91.16 % |
7751646 |
33.00 % |
| q20,qd2 |
38220641 |
6.03 % |
23463891 |
3.85 % |
14756750 |
62.83 % |
| q20,mq40 |
13032222 |
2.06 % |
12747910 |
2.09 % |
284312 |
1.21 % |
| qd2 |
12628620 |
1.99 % |
12407544 |
2.03 % |
221076 |
0.94 % |
| q20,qd2,mq40 |
4061151 |
0.64 % |
3796560 |
0.62 % |
264591 |
1.13 % |
| mq40 |
1617907 |
0.26 % |
1442689 |
0.24 % |
175218 |
0.75 % |
| qd2,mq40 |
78313 |
0.01 % |
67566 |
0.01 % |
10747 |
0.05 % |
| q20,qd2,fs60 |
8889 |
0.00 % |
0 |
0.00 % |
8889 |
0.04 % |
| fs60 |
6513 |
0.00 % |
0 |
0.00 % |
6513 |
0.03 % |
| qd2,fs60 |
6058 |
0.00 % |
0 |
0.00 % |
6058 |
0.03 % |
| qd2,fs60,mq40 |
1452 |
0.00 % |
0 |
0.00 % |
1452 |
0.01 % |
| fs60,mq40 |
380 |
0.00 % |
0 |
0.00 % |
380 |
0.00 % |
| q20,qd2,fs60,mq40 |
316 |
0.00 % |
0 |
0.00 % |
316 |
0.00 % |
| q20,fs60 |
13 |
0.00 % |
0 |
0.00 % |
13 |
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 |
9911180 |
29.51 % |
| Transition |
G>A |
All |
2937263 |
8.74 % |
| Transition |
T>C |
All |
7489121 |
22.30 % |
| Transition |
C>T |
All |
2969691 |
8.84 % |
| Transversion |
A>C |
All |
792515 |
2.36 % |
| Transversion |
C>A |
All |
1813840 |
5.40 % |
| Transversion |
T>G |
All |
948696 |
2.82 % |
| Transversion |
G>T |
All |
1685909 |
5.02 % |
| Transversion |
A>T |
All |
1724230 |
5.13 % |
| Transversion |
T>A |
All |
1871639 |
5.57 % |
| Transversion |
C>G |
All |
792571 |
2.36 % |
| Transversion |
G>C |
All |
652770 |
1.94 % |
| |
|
|
|
|
| Transition |
A>G |
Passed |
553018 |
20.64 % |
| Transition |
G>A |
Passed |
381928 |
14.26 % |
| Transition |
T>C |
Passed |
479267 |
17.89 % |
| Transition |
C>T |
Passed |
385830 |
14.40 % |
| Transversion |
A>C |
Passed |
105312 |
3.93 % |
| Transversion |
C>A |
Passed |
122336 |
4.57 % |
| Transversion |
T>G |
Passed |
110335 |
4.12 % |
| Transversion |
G>T |
Passed |
119416 |
4.46 % |
| Transversion |
A>T |
Passed |
108468 |
4.05 % |
| Transversion |
T>A |
Passed |
111132 |
4.15 % |
| Transversion |
C>G |
Passed |
102205 |
3.82 % |
| Transversion |
G>C |
Passed |
99547 |
3.72 % |
| |
|
|
|
|
| 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 |
2.27 |
23307255 |
10282170 |
| Passed |
2.05 |
1800043 |
878751 |
| dbSNPAll |
0 |
0 |
0 |
| dbSNPPassed |
0 |
0 |
0 |