/EXTERNAL BLUEPRINT/variants/K006286_14_lane_gembs
BACK
SAMPLE K006286_14_lane_gembs
Variant counts
| Type |
Total |
Pass |
% |
| SNPs |
1133253769 |
675519907 |
59.61 % |
| Multiallelic |
0 |
0 |
0.00 % |
VCF Filtering Stats
| Type |
#Sites |
% |
#Non-Variant Sites |
% |
#Variant Sites |
% |
| All |
1133253769 |
100% |
1122378142 |
99.04 % |
10875627 |
0.96 % |
| |
|
|
|
|
|
|
| Passed |
677929425 |
59.82 % |
673965370 |
60.05 % |
3964055 |
0.58 % |
| Filtered |
455324344 |
40.18 % |
448412772 |
39.95 % |
6911572 |
1.02 % |
| |
|
|
|
|
|
|
| q20 |
413680094 |
90.85 % |
412030508 |
91.89 % |
1649586 |
23.87 % |
| q20,qd2 |
18142241 |
3.98 % |
13396933 |
2.99 % |
4745308 |
68.66 % |
| q20,mq40 |
13780658 |
3.03 % |
13689316 |
3.05 % |
91342 |
1.32 % |
| mq40 |
5481573 |
1.20 % |
5308738 |
1.18 % |
172835 |
2.50 % |
| q20,qd2,mq40 |
2571658 |
0.56 % |
2429427 |
0.54 % |
142231 |
2.06 % |
| qd2 |
1604101 |
0.35 % |
1507208 |
0.34 % |
96893 |
1.40 % |
| qd2,mq40 |
60189 |
0.01 % |
50642 |
0.01 % |
9547 |
0.14 % |
| qd2,fs60,mq40 |
964 |
0.00 % |
0 |
0.00 % |
964 |
0.01 % |
| fs60 |
935 |
0.00 % |
0 |
0.00 % |
935 |
0.01 % |
| qd2,fs60 |
680 |
0.00 % |
0 |
0.00 % |
680 |
0.01 % |
| q20,qd2,fs60 |
613 |
0.00 % |
0 |
0.00 % |
613 |
0.01 % |
| fs60,mq40 |
442 |
0.00 % |
0 |
0.00 % |
442 |
0.01 % |
| q20,qd2,fs60,mq40 |
193 |
0.00 % |
0 |
0.00 % |
193 |
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 |
3919217 |
30.70 % |
| Transition |
G>A |
All |
1227458 |
9.62 % |
| Transition |
T>C |
All |
3832811 |
30.03 % |
| Transition |
C>T |
All |
1216716 |
9.53 % |
| Transversion |
A>C |
All |
214377 |
1.68 % |
| Transversion |
C>A |
All |
511664 |
4.01 % |
| Transversion |
T>G |
All |
219684 |
1.72 % |
| Transversion |
G>T |
All |
499812 |
3.92 % |
| Transversion |
A>T |
All |
358924 |
2.81 % |
| Transversion |
T>A |
All |
350965 |
2.75 % |
| Transversion |
C>G |
All |
208791 |
1.64 % |
| Transversion |
G>C |
All |
203692 |
1.60 % |
| |
|
|
|
|
| Transition |
A>G |
Passed |
407777 |
18.16 % |
| Transition |
G>A |
Passed |
369660 |
16.46 % |
| Transition |
T>C |
Passed |
407331 |
18.14 % |
| Transition |
C>T |
Passed |
371602 |
16.55 % |
| Transversion |
A>C |
Passed |
89892 |
4.00 % |
| Transversion |
C>A |
Passed |
86229 |
3.84 % |
| Transversion |
T>G |
Passed |
89341 |
3.98 % |
| Transversion |
G>T |
Passed |
85412 |
3.80 % |
| Transversion |
A>T |
Passed |
61616 |
2.74 % |
| Transversion |
T>A |
Passed |
61470 |
2.74 % |
| Transversion |
C>G |
Passed |
106950 |
4.76 % |
| Transversion |
G>C |
Passed |
107956 |
4.81 % |
| |
|
|
|
|
| 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 |
3.97 |
10196202 |
2567909 |
| Passed |
2.26 |
1556370 |
688866 |
| dbSNPAll |
0 |
0 |
0 |
| dbSNPPassed |
0 |
0 |
0 |