/EXTERNAL BLUEPRINT/variants/K006355_9_lane_gembs
BACK
SAMPLE K006355_9_lane_gembs
Variant counts
| Type |
Total |
Pass |
% |
| SNPs |
1110315984 |
623756419 |
56.18 % |
| Multiallelic |
0 |
0 |
0.00 % |
VCF Filtering Stats
| Type |
#Sites |
% |
#Non-Variant Sites |
% |
#Variant Sites |
% |
| All |
1110315984 |
100% |
1095746214 |
98.69 % |
14569770 |
1.31 % |
| |
|
|
|
|
|
|
| Passed |
625358413 |
56.32 % |
622466801 |
56.81 % |
2891612 |
0.46 % |
| Filtered |
484957571 |
43.68 % |
473279413 |
43.19 % |
11678158 |
1.87 % |
| |
|
|
|
|
|
|
| q20 |
413317806 |
85.23 % |
411885503 |
87.03 % |
1432303 |
12.26 % |
| q20,qd2 |
46299742 |
9.55 % |
36586824 |
7.73 % |
9712918 |
83.17 % |
| q20,mq40 |
14504213 |
2.99 % |
14402678 |
3.04 % |
101535 |
0.87 % |
| mq40 |
5699430 |
1.18 % |
5546892 |
1.17 % |
152538 |
1.31 % |
| q20,qd2,mq40 |
3319733 |
0.68 % |
3134229 |
0.66 % |
185504 |
1.59 % |
| qd2 |
1735605 |
0.36 % |
1659139 |
0.35 % |
76466 |
0.65 % |
| qd2,mq40 |
74883 |
0.02 % |
64148 |
0.01 % |
10735 |
0.09 % |
| q20,qd2,fs60 |
2064 |
0.00 % |
0 |
0.00 % |
2064 |
0.02 % |
| fs60 |
1198 |
0.00 % |
0 |
0.00 % |
1198 |
0.01 % |
| qd2,fs60,mq40 |
1088 |
0.00 % |
0 |
0.00 % |
1088 |
0.01 % |
| qd2,fs60 |
835 |
0.00 % |
0 |
0.00 % |
835 |
0.01 % |
| q20,qd2,fs60,mq40 |
519 |
0.00 % |
0 |
0.00 % |
519 |
0.00 % |
| fs60,mq40 |
452 |
0.00 % |
0 |
0.00 % |
452 |
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 |
2917995 |
17.22 % |
| Transition |
G>A |
All |
4216722 |
24.88 % |
| Transition |
T>C |
All |
2818874 |
16.63 % |
| Transition |
C>T |
All |
4112739 |
24.27 % |
| Transversion |
A>C |
All |
211097 |
1.25 % |
| Transversion |
C>A |
All |
587950 |
3.47 % |
| Transversion |
T>G |
All |
221106 |
1.30 % |
| Transversion |
G>T |
All |
585233 |
3.45 % |
| Transversion |
A>T |
All |
455916 |
2.69 % |
| Transversion |
T>A |
All |
449178 |
2.65 % |
| Transversion |
C>G |
All |
188306 |
1.11 % |
| Transversion |
G>C |
All |
180798 |
1.07 % |
| |
|
|
|
|
| Transition |
A>G |
Passed |
358090 |
18.61 % |
| Transition |
G>A |
Passed |
329399 |
17.12 % |
| Transition |
T>C |
Passed |
357738 |
18.59 % |
| Transition |
C>T |
Passed |
329247 |
17.11 % |
| Transversion |
A>C |
Passed |
73859 |
3.84 % |
| Transversion |
C>A |
Passed |
67250 |
3.50 % |
| Transversion |
T>G |
Passed |
73487 |
3.82 % |
| Transversion |
G>T |
Passed |
67519 |
3.51 % |
| Transversion |
A>T |
Passed |
45876 |
2.38 % |
| Transversion |
T>A |
Passed |
45891 |
2.39 % |
| Transversion |
C>G |
Passed |
87763 |
4.56 % |
| Transversion |
G>C |
Passed |
88010 |
4.57 % |
| |
|
|
|
|
| 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 |
4.88 |
14066330 |
2879584 |
| Passed |
2.50 |
1374474 |
549655 |
| dbSNPAll |
0 |
0 |
0 |
| dbSNPPassed |
0 |
0 |
0 |