/EXTERNAL BLUEPRINT/variants/K011948_K011949_K011950_K011951_K011952_K011953_K011954_K011955_K011971_9_lane_gembs
BACK
SAMPLE K011948_K011949_K011950_K011951_K011952_K011953_K011954_K011955_K011971_9_lane_gembs
Variant counts
| Type |
Total |
Pass |
% |
| SNPs |
640653976 |
913386 |
0.14 % |
| Multiallelic |
0 |
0 |
0.00 % |
VCF Filtering Stats
| Type |
#Sites |
% |
#Non-Variant Sites |
% |
#Variant Sites |
% |
| All |
640653976 |
100% |
634235022 |
99.00 % |
6418954 |
1.00 % |
| |
|
|
|
|
|
|
| Passed |
4424951 |
0.69 % |
795393 |
0.13 % |
3629558 |
82.02 % |
| Filtered |
636229025 |
99.31 % |
633439629 |
99.87 % |
2789396 |
63.04 % |
| |
|
|
|
|
|
|
| q20 |
501838915 |
78.88 % |
499789591 |
78.90 % |
2049324 |
73.47 % |
| q20,qd2 |
79417039 |
12.48 % |
79051353 |
12.48 % |
365686 |
13.11 % |
| q20,mq40 |
42209991 |
6.63 % |
42059409 |
6.64 % |
150582 |
5.40 % |
| q20,qd2,mq40 |
12515908 |
1.97 % |
12489495 |
1.97 % |
26413 |
0.95 % |
| mq40 |
244463 |
0.04 % |
47339 |
0.01 % |
197124 |
7.07 % |
| qd2 |
2215 |
0.00 % |
2075 |
0.00 % |
140 |
0.01 % |
| qd2,mq40 |
472 |
0.00 % |
367 |
0.00 % |
105 |
0.00 % |
| fs60,mq40 |
9 |
0.00 % |
0 |
0.00 % |
9 |
0.00 % |
| qd2,fs60 |
8 |
0.00 % |
0 |
0.00 % |
8 |
0.00 % |
| fs60 |
4 |
0.00 % |
0 |
0.00 % |
4 |
0.00 % |
| qd2,fs60,mq40 |
1 |
0.00 % |
0 |
0.00 % |
1 |
0.00 % |
| q20,fs60 |
0 |
0.00 % |
0 |
0.00 % |
0 |
0.00 % |
| q20,qd2,fs60 |
0 |
0.00 % |
0 |
0.00 % |
0 |
0.00 % |
| q20,fs60,mq40 |
0 |
0.00 % |
0 |
0.00 % |
0 |
0.00 % |
| q20,qd2,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 |
2356878 |
21.31 % |
| Transition |
G>A |
All |
824652 |
7.46 % |
| Transition |
T>C |
All |
3124458 |
28.25 % |
| Transition |
C>T |
All |
427494 |
3.87 % |
| Transversion |
A>C |
All |
447220 |
4.04 % |
| Transversion |
C>A |
All |
691466 |
6.25 % |
| Transversion |
T>G |
All |
456028 |
4.12 % |
| Transversion |
G>T |
All |
650065 |
5.88 % |
| Transversion |
A>T |
All |
549745 |
4.97 % |
| Transversion |
T>A |
All |
734762 |
6.64 % |
| Transversion |
C>G |
All |
357081 |
3.23 % |
| Transversion |
G>C |
All |
438532 |
3.97 % |
| |
|
|
|
|
| Transition |
A>G |
Passed |
17358 |
14.82 % |
| Transition |
G>A |
Passed |
15115 |
12.91 % |
| Transition |
T>C |
Passed |
28079 |
23.98 % |
| Transition |
C>T |
Passed |
6488 |
5.54 % |
| Transversion |
A>C |
Passed |
6482 |
5.54 % |
| Transversion |
C>A |
Passed |
7343 |
6.27 % |
| Transversion |
T>G |
Passed |
5785 |
4.94 % |
| Transversion |
G>T |
Passed |
4858 |
4.15 % |
| Transversion |
A>T |
Passed |
3294 |
2.81 % |
| Transversion |
T>A |
Passed |
7346 |
6.27 % |
| Transversion |
C>G |
Passed |
6333 |
5.41 % |
| Transversion |
G>C |
Passed |
8611 |
7.35 % |
| |
|
|
|
|
| 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 |
1.56 |
6733482 |
4324899 |
| Passed |
1.34 |
67040 |
50052 |
| dbSNPAll |
0 |
0 |
0 |
| dbSNPPassed |
0 |
0 |
0 |