/EXTERNAL BLUEPRINT/variants/K006338_12_lane_gembs
BACK
SAMPLE K006338_12_lane_gembs
Variant counts
| Type |
Total |
Pass |
% |
| SNPs |
1113115508 |
653207342 |
58.68 % |
| Multiallelic |
0 |
0 |
0.00 % |
VCF Filtering Stats
| Type |
#Sites |
% |
#Non-Variant Sites |
% |
#Variant Sites |
% |
| All |
1113115508 |
100% |
1094727752 |
98.35 % |
18387756 |
1.65 % |
| |
|
|
|
|
|
|
| Passed |
654757840 |
58.82 % |
651874806 |
59.55 % |
2883034 |
0.44 % |
| Filtered |
458357668 |
41.18 % |
442852946 |
40.45 % |
15504722 |
2.37 % |
| |
|
|
|
|
|
|
| q20 |
380235909 |
82.96 % |
378530002 |
85.48 % |
1705907 |
11.00 % |
| q20,qd2 |
50552659 |
11.03 % |
37354979 |
8.44 % |
13197680 |
85.12 % |
| q20,mq40 |
14770959 |
3.22 % |
14657158 |
3.31 % |
113801 |
0.73 % |
| mq40 |
7232731 |
1.58 % |
7066394 |
1.60 % |
166337 |
1.07 % |
| q20,qd2,mq40 |
3315665 |
0.72 % |
3106992 |
0.70 % |
208673 |
1.35 % |
| qd2 |
2150625 |
0.47 % |
2058686 |
0.46 % |
91939 |
0.59 % |
| qd2,mq40 |
90566 |
0.02 % |
78735 |
0.02 % |
11831 |
0.08 % |
| q20,qd2,fs60 |
3046 |
0.00 % |
0 |
0.00 % |
3046 |
0.02 % |
| fs60 |
2048 |
0.00 % |
0 |
0.00 % |
2048 |
0.01 % |
| qd2,fs60 |
1222 |
0.00 % |
0 |
0.00 % |
1222 |
0.01 % |
| qd2,fs60,mq40 |
1157 |
0.00 % |
0 |
0.00 % |
1157 |
0.01 % |
| q20,qd2,fs60,mq40 |
590 |
0.00 % |
0 |
0.00 % |
590 |
0.00 % |
| fs60,mq40 |
484 |
0.00 % |
0 |
0.00 % |
484 |
0.00 % |
| q20,fs60 |
5 |
0.00 % |
0 |
0.00 % |
5 |
0.00 % |
| q20,fs60,mq40 |
2 |
0.00 % |
0 |
0.00 % |
2 |
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 |
3087909 |
13.27 % |
| Transition |
G>A |
All |
7277303 |
31.28 % |
| Transition |
T>C |
All |
2913842 |
12.52 % |
| Transition |
C>T |
All |
7098361 |
30.51 % |
| Transversion |
A>C |
All |
225819 |
0.97 % |
| Transversion |
C>A |
All |
576289 |
2.48 % |
| Transversion |
T>G |
All |
241327 |
1.04 % |
| Transversion |
G>T |
All |
574220 |
2.47 % |
| Transversion |
A>T |
All |
448622 |
1.93 % |
| Transversion |
T>A |
All |
441224 |
1.90 % |
| Transversion |
C>G |
All |
195855 |
0.84 % |
| Transversion |
G>C |
All |
187629 |
0.81 % |
| |
|
|
|
|
| Transition |
A>G |
Passed |
373747 |
18.62 % |
| Transition |
G>A |
Passed |
345246 |
17.20 % |
| Transition |
T>C |
Passed |
372487 |
18.56 % |
| Transition |
C>T |
Passed |
345894 |
17.24 % |
| Transversion |
A>C |
Passed |
76682 |
3.82 % |
| Transversion |
C>A |
Passed |
69608 |
3.47 % |
| Transversion |
T>G |
Passed |
75956 |
3.78 % |
| Transversion |
G>T |
Passed |
70211 |
3.50 % |
| Transversion |
A>T |
Passed |
47977 |
2.39 % |
| Transversion |
T>A |
Passed |
47892 |
2.39 % |
| Transversion |
C>G |
Passed |
90155 |
4.49 % |
| Transversion |
G>C |
Passed |
90954 |
4.53 % |
| |
|
|
|
|
| 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 |
7.05 |
20377415 |
2890985 |
| Passed |
2.52 |
1437374 |
569435 |
| dbSNPAll |
0 |
0 |
0 |
| dbSNPPassed |
0 |
0 |
0 |