/EXTERNAL BLUEPRINT/variants/K006415_14_lane_gembs
BACK
SAMPLE K006415_14_lane_gembs
Variant counts
| Type |
Total |
Pass |
% |
| SNPs |
1157877698 |
1040932342 |
89.90 % |
| Multiallelic |
0 |
0 |
0.00 % |
VCF Filtering Stats
| Type |
#Sites |
% |
#Non-Variant Sites |
% |
#Variant Sites |
% |
| All |
1157877698 |
100% |
1144981896 |
98.89 % |
12895802 |
1.11 % |
| |
|
|
|
|
|
|
| Passed |
1041968929 |
89.99 % |
1038441004 |
90.69 % |
3527925 |
0.34 % |
| Filtered |
115908769 |
10.01 % |
106540892 |
9.31 % |
9367877 |
0.90 % |
| |
|
|
|
|
|
|
| q20 |
79934963 |
68.96 % |
79128657 |
74.27 % |
806306 |
8.61 % |
| q20,mq40 |
13099020 |
11.30 % |
12974882 |
12.18 % |
124138 |
1.33 % |
| q20,qd2 |
12803078 |
11.05 % |
4962358 |
4.66 % |
7840720 |
83.70 % |
| mq40 |
4242621 |
3.66 % |
4017821 |
3.77 % |
224800 |
2.40 % |
| q20,qd2,mq40 |
3146882 |
2.71 % |
2923440 |
2.74 % |
223442 |
2.39 % |
| qd2 |
2630125 |
2.27 % |
2491942 |
2.34 % |
138183 |
1.48 % |
| qd2,mq40 |
50623 |
0.04 % |
41792 |
0.04 % |
8831 |
0.09 % |
| qd2,fs60,mq40 |
680 |
0.00 % |
0 |
0.00 % |
680 |
0.01 % |
| fs60,mq40 |
326 |
0.00 % |
0 |
0.00 % |
326 |
0.00 % |
| qd2,fs60 |
168 |
0.00 % |
0 |
0.00 % |
168 |
0.00 % |
| fs60 |
150 |
0.00 % |
0 |
0.00 % |
150 |
0.00 % |
| q20,qd2,fs60,mq40 |
87 |
0.00 % |
0 |
0.00 % |
87 |
0.00 % |
| q20,qd2,fs60 |
43 |
0.00 % |
0 |
0.00 % |
43 |
0.00 % |
| q20,fs60,mq40 |
2 |
0.00 % |
0 |
0.00 % |
2 |
0.00 % |
| q20,fs60 |
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 |
4661737 |
32.01 % |
| Transition |
G>A |
All |
1078314 |
7.40 % |
| Transition |
T>C |
All |
4611916 |
31.66 % |
| Transition |
C>T |
All |
1080979 |
7.42 % |
| Transversion |
A>C |
All |
225391 |
1.55 % |
| Transversion |
C>A |
All |
652259 |
4.48 % |
| Transversion |
T>G |
All |
227294 |
1.56 % |
| Transversion |
G>T |
All |
643808 |
4.42 % |
| Transversion |
A>T |
All |
480842 |
3.30 % |
| Transversion |
T>A |
All |
477167 |
3.28 % |
| Transversion |
C>G |
All |
212163 |
1.46 % |
| Transversion |
G>C |
All |
212910 |
1.46 % |
| |
|
|
|
|
| Transition |
A>G |
Passed |
633492 |
17.29 % |
| Transition |
G>A |
Passed |
595409 |
16.25 % |
| Transition |
T>C |
Passed |
635363 |
17.34 % |
| Transition |
C>T |
Passed |
598859 |
16.35 % |
| Transversion |
A>C |
Passed |
152373 |
4.16 % |
| Transversion |
C>A |
Passed |
159591 |
4.36 % |
| Transversion |
T>G |
Passed |
152944 |
4.18 % |
| Transversion |
G>T |
Passed |
159859 |
4.36 % |
| Transversion |
A>T |
Passed |
135544 |
3.70 % |
| Transversion |
T>A |
Passed |
135707 |
3.70 % |
| Transversion |
C>G |
Passed |
151921 |
4.15 % |
| Transversion |
G>C |
Passed |
152163 |
4.15 % |
| |
|
|
|
|
| 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 |
3.65 |
11432946 |
3131834 |
| Passed |
2.05 |
2463123 |
1200102 |
| dbSNPAll |
0 |
0 |
0 |
| dbSNPPassed |
0 |
0 |
0 |