/EXTERNAL BLUEPRINT/variants/K006309_K006319_21_lane_gembs
BACK
SAMPLE K006309_K006319_21_lane_gembs
Variant counts
| Type |
Total |
Pass |
% |
| SNPs |
1034213086 |
440737397 |
42.62 % |
| Multiallelic |
0 |
0 |
0.00 % |
VCF Filtering Stats
| Type |
#Sites |
% |
#Non-Variant Sites |
% |
#Variant Sites |
% |
| All |
1034213086 |
100% |
1017003307 |
98.34 % |
17209779 |
1.66 % |
| |
|
|
|
|
|
|
| Passed |
442740563 |
42.81 % |
439841889 |
43.25 % |
2898674 |
0.65 % |
| Filtered |
591472523 |
57.19 % |
577161418 |
56.75 % |
14311105 |
3.23 % |
| |
|
|
|
|
|
|
| q20 |
477844189 |
80.79 % |
475243820 |
82.34 % |
2600369 |
18.17 % |
| q20,qd2 |
70918720 |
11.99 % |
59738076 |
10.35 % |
11180644 |
78.13 % |
| q20,mq40 |
16730533 |
2.83 % |
16634794 |
2.88 % |
95739 |
0.67 % |
| qd2 |
15057560 |
2.55 % |
14953197 |
2.59 % |
104363 |
0.73 % |
| mq40 |
6735031 |
1.14 % |
6583413 |
1.14 % |
151618 |
1.06 % |
| q20,qd2,mq40 |
4068207 |
0.69 % |
3918744 |
0.68 % |
149463 |
1.04 % |
| qd2,mq40 |
102056 |
0.02 % |
89374 |
0.02 % |
12682 |
0.09 % |
| qd2,fs60 |
5340 |
0.00 % |
0 |
0.00 % |
5340 |
0.04 % |
| q20,qd2,fs60 |
4685 |
0.00 % |
0 |
0.00 % |
4685 |
0.03 % |
| qd2,fs60,mq40 |
2436 |
0.00 % |
0 |
0.00 % |
2436 |
0.02 % |
| fs60 |
2186 |
0.00 % |
0 |
0.00 % |
2186 |
0.02 % |
| q20,qd2,fs60,mq40 |
921 |
0.00 % |
0 |
0.00 % |
921 |
0.01 % |
| fs60,mq40 |
652 |
0.00 % |
0 |
0.00 % |
652 |
0.00 % |
| q20,fs60 |
6 |
0.00 % |
0 |
0.00 % |
6 |
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 |
3689947 |
12.35 % |
| Transition |
G>A |
All |
10267439 |
34.37 % |
| Transition |
T>C |
All |
2704156 |
9.05 % |
| Transition |
C>T |
All |
10097551 |
33.80 % |
| Transversion |
A>C |
All |
225978 |
0.76 % |
| Transversion |
C>A |
All |
597907 |
2.00 % |
| Transversion |
T>G |
All |
321260 |
1.08 % |
| Transversion |
G>T |
All |
548406 |
1.84 % |
| Transversion |
A>T |
All |
454254 |
1.52 % |
| Transversion |
T>A |
All |
520905 |
1.74 % |
| Transversion |
C>G |
All |
244891 |
0.82 % |
| Transversion |
G>C |
All |
201579 |
0.67 % |
| |
|
|
|
|
| Transition |
A>G |
Passed |
268324 |
20.60 % |
| Transition |
G>A |
Passed |
219404 |
16.84 % |
| Transition |
T>C |
Passed |
263656 |
20.24 % |
| Transition |
C>T |
Passed |
218668 |
16.79 % |
| Transversion |
A>C |
Passed |
43906 |
3.37 % |
| Transversion |
C>A |
Passed |
39122 |
3.00 % |
| Transversion |
T>G |
Passed |
43900 |
3.37 % |
| Transversion |
G>T |
Passed |
39092 |
3.00 % |
| Transversion |
A>T |
Passed |
23885 |
1.83 % |
| Transversion |
T>A |
Passed |
23398 |
1.80 % |
| Transversion |
C>G |
Passed |
59841 |
4.59 % |
| Transversion |
G>C |
Passed |
59441 |
4.56 % |
| |
|
|
|
|
| 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 |
8.59 |
26759093 |
3115180 |
| Passed |
2.92 |
970052 |
332585 |
| dbSNPAll |
0 |
0 |
0 |
| dbSNPPassed |
0 |
0 |
0 |