/EXTERNAL BLUEPRINT/variants/K006308_K006318_18_lane_gembs
BACK
SAMPLE K006308_K006318_18_lane_gembs
Variant counts
| Type |
Total |
Pass |
% |
| SNPs |
1063887704 |
464928529 |
43.70 % |
| Multiallelic |
0 |
0 |
0.00 % |
VCF Filtering Stats
| Type |
#Sites |
% |
#Non-Variant Sites |
% |
#Variant Sites |
% |
| All |
1063887704 |
100% |
1047392385 |
98.45 % |
16495319 |
1.55 % |
| |
|
|
|
|
|
|
| Passed |
466950557 |
43.89 % |
463867340 |
44.29 % |
3083217 |
0.66 % |
| Filtered |
596937147 |
56.11 % |
583525045 |
55.71 % |
13412102 |
2.87 % |
| |
|
|
|
|
|
|
| q20 |
499686974 |
83.71 % |
497314247 |
85.23 % |
2372727 |
17.69 % |
| q20,qd2 |
65308346 |
10.94 % |
54779547 |
9.39 % |
10528799 |
78.50 % |
| q20,mq40 |
14819664 |
2.48 % |
14718339 |
2.52 % |
101325 |
0.76 % |
| qd2 |
9410718 |
1.58 % |
9304302 |
1.59 % |
106416 |
0.79 % |
| q20,qd2,mq40 |
4243787 |
0.71 % |
4102741 |
0.70 % |
141046 |
1.05 % |
| mq40 |
3363076 |
0.56 % |
3226395 |
0.55 % |
136681 |
1.02 % |
| qd2,mq40 |
91509 |
0.02 % |
79474 |
0.01 % |
12035 |
0.09 % |
| q20,qd2,fs60 |
3800 |
0.00 % |
0 |
0.00 % |
3800 |
0.03 % |
| qd2,fs60 |
3763 |
0.00 % |
0 |
0.00 % |
3763 |
0.03 % |
| qd2,fs60,mq40 |
2268 |
0.00 % |
0 |
0.00 % |
2268 |
0.02 % |
| fs60 |
1728 |
0.00 % |
0 |
0.00 % |
1728 |
0.01 % |
| q20,qd2,fs60,mq40 |
932 |
0.00 % |
0 |
0.00 % |
932 |
0.01 % |
| fs60,mq40 |
581 |
0.00 % |
0 |
0.00 % |
581 |
0.00 % |
| q20,fs60 |
1 |
0.00 % |
0 |
0.00 % |
1 |
0.00 % |
| q20,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 |
3316351 |
12.79 % |
| Transition |
G>A |
All |
8136036 |
31.38 % |
| Transition |
T>C |
All |
2877616 |
11.10 % |
| Transition |
C>T |
All |
8097609 |
31.23 % |
| Transversion |
A>C |
All |
241929 |
0.93 % |
| Transversion |
C>A |
All |
690373 |
2.66 % |
| Transversion |
T>G |
All |
293288 |
1.13 % |
| Transversion |
G>T |
All |
669161 |
2.58 % |
| Transversion |
A>T |
All |
569968 |
2.20 % |
| Transversion |
T>A |
All |
591772 |
2.28 % |
| Transversion |
C>G |
All |
236580 |
0.91 % |
| Transversion |
G>C |
All |
210435 |
0.81 % |
| |
|
|
|
|
| Transition |
A>G |
Passed |
302141 |
20.27 % |
| Transition |
G>A |
Passed |
250566 |
16.81 % |
| Transition |
T>C |
Passed |
297742 |
19.98 % |
| Transition |
C>T |
Passed |
248174 |
16.65 % |
| Transversion |
A>C |
Passed |
51468 |
3.45 % |
| Transversion |
C>A |
Passed |
47176 |
3.17 % |
| Transversion |
T>G |
Passed |
50726 |
3.40 % |
| Transversion |
G>T |
Passed |
47002 |
3.15 % |
| Transversion |
A>T |
Passed |
30724 |
2.06 % |
| Transversion |
T>A |
Passed |
30844 |
2.07 % |
| Transversion |
C>G |
Passed |
66773 |
4.48 % |
| Transversion |
G>C |
Passed |
66933 |
4.49 % |
| |
|
|
|
|
| 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 |
6.40 |
22427612 |
3503506 |
| Passed |
2.81 |
1098623 |
391646 |
| dbSNPAll |
0 |
0 |
0 |
| dbSNPPassed |
0 |
0 |
0 |