/EXTERNAL BLUEPRINT/variants/K006341_12_lane_gembs
BACK
SAMPLE K006341_12_lane_gembs
Variant counts
| Type |
Total |
Pass |
% |
| SNPs |
1116267696 |
658196221 |
58.96 % |
| Multiallelic |
0 |
0 |
0.00 % |
VCF Filtering Stats
| Type |
#Sites |
% |
#Non-Variant Sites |
% |
#Variant Sites |
% |
| All |
1116267696 |
100% |
1101988371 |
98.72 % |
14279325 |
1.28 % |
| |
|
|
|
|
|
|
| Passed |
659901379 |
59.12 % |
656794212 |
59.60 % |
3107167 |
0.47 % |
| Filtered |
456366317 |
40.88 % |
445194159 |
40.40 % |
11172158 |
1.69 % |
| |
|
|
|
|
|
|
| q20 |
389007107 |
85.24 % |
387456618 |
87.03 % |
1550489 |
13.88 % |
| q20,qd2 |
40840514 |
8.95 % |
31794799 |
7.14 % |
9045715 |
80.97 % |
| q20,mq40 |
14392004 |
3.15 % |
14281287 |
3.21 % |
110717 |
0.99 % |
| mq40 |
6194436 |
1.36 % |
6033173 |
1.36 % |
161263 |
1.44 % |
| q20,qd2,mq40 |
3264786 |
0.72 % |
3059708 |
0.69 % |
205078 |
1.84 % |
| qd2 |
2584790 |
0.57 % |
2501693 |
0.56 % |
83097 |
0.74 % |
| qd2,mq40 |
76935 |
0.02 % |
66881 |
0.02 % |
10054 |
0.09 % |
| q20,qd2,fs60 |
1749 |
0.00 % |
0 |
0.00 % |
1749 |
0.02 % |
| qd2,fs60,mq40 |
1170 |
0.00 % |
0 |
0.00 % |
1170 |
0.01 % |
| fs60 |
1157 |
0.00 % |
0 |
0.00 % |
1157 |
0.01 % |
| qd2,fs60 |
657 |
0.00 % |
0 |
0.00 % |
657 |
0.01 % |
| fs60,mq40 |
519 |
0.00 % |
0 |
0.00 % |
519 |
0.00 % |
| q20,qd2,fs60,mq40 |
490 |
0.00 % |
0 |
0.00 % |
490 |
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 |
3146143 |
19.23 % |
| Transition |
G>A |
All |
3580273 |
21.88 % |
| Transition |
T>C |
All |
2997218 |
18.31 % |
| Transition |
C>T |
All |
3490185 |
21.33 % |
| Transversion |
A>C |
All |
219945 |
1.34 % |
| Transversion |
C>A |
All |
706038 |
4.31 % |
| Transversion |
T>G |
All |
233340 |
1.43 % |
| Transversion |
G>T |
All |
706296 |
4.32 % |
| Transversion |
A>T |
All |
456422 |
2.79 % |
| Transversion |
T>A |
All |
445175 |
2.72 % |
| Transversion |
C>G |
All |
196377 |
1.20 % |
| Transversion |
G>C |
All |
187439 |
1.15 % |
| |
|
|
|
|
| Transition |
A>G |
Passed |
378263 |
18.26 % |
| Transition |
G>A |
Passed |
358404 |
17.30 % |
| Transition |
T>C |
Passed |
377084 |
18.20 % |
| Transition |
C>T |
Passed |
359944 |
17.38 % |
| Transversion |
A>C |
Passed |
79106 |
3.82 % |
| Transversion |
C>A |
Passed |
74808 |
3.61 % |
| Transversion |
T>G |
Passed |
78615 |
3.80 % |
| Transversion |
G>T |
Passed |
75697 |
3.65 % |
| Transversion |
A>T |
Passed |
51269 |
2.48 % |
| Transversion |
T>A |
Passed |
51360 |
2.48 % |
| Transversion |
C>G |
Passed |
93063 |
4.49 % |
| Transversion |
G>C |
Passed |
93844 |
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 |
4.19 |
13213819 |
3151032 |
| Passed |
2.47 |
1473695 |
597762 |
| dbSNPAll |
0 |
0 |
0 |
| dbSNPPassed |
0 |
0 |
0 |