/EXTERNAL BLUEPRINT/variants/K006373_15_lane_gembs
BACK
SAMPLE K006373_15_lane_gembs
Variant counts
| Type |
Total |
Pass |
% |
| SNPs |
1151066101 |
1056371634 |
91.77 % |
| Multiallelic |
0 |
0 |
0.00 % |
VCF Filtering Stats
| Type |
#Sites |
% |
#Non-Variant Sites |
% |
#Variant Sites |
% |
| All |
1151066101 |
100% |
1140122802 |
99.05 % |
10943299 |
0.95 % |
| |
|
|
|
|
|
|
| Passed |
1057129550 |
91.84 % |
1053886103 |
92.44 % |
3243447 |
0.31 % |
| Filtered |
93936551 |
8.16 % |
86236699 |
7.56 % |
7699852 |
0.73 % |
| |
|
|
|
|
|
|
| q20 |
62604401 |
66.65 % |
61989351 |
71.88 % |
615050 |
7.99 % |
| q20,mq40 |
12488105 |
13.29 % |
12384891 |
14.36 % |
103214 |
1.34 % |
| q20,qd2 |
10094029 |
10.75 % |
3643428 |
4.22 % |
6450601 |
83.78 % |
| mq40 |
4129706 |
4.40 % |
3928523 |
4.56 % |
201183 |
2.61 % |
| q20,qd2,mq40 |
3005894 |
3.20 % |
2833049 |
3.29 % |
172845 |
2.24 % |
| qd2 |
1570134 |
1.67 % |
1422780 |
1.65 % |
147354 |
1.91 % |
| qd2,mq40 |
43085 |
0.05 % |
34677 |
0.04 % |
8408 |
0.11 % |
| qd2,fs60,mq40 |
600 |
0.00 % |
0 |
0.00 % |
600 |
0.01 % |
| fs60,mq40 |
268 |
0.00 % |
0 |
0.00 % |
268 |
0.00 % |
| qd2,fs60 |
138 |
0.00 % |
0 |
0.00 % |
138 |
0.00 % |
| fs60 |
115 |
0.00 % |
0 |
0.00 % |
115 |
0.00 % |
| q20,qd2,fs60,mq40 |
58 |
0.00 % |
0 |
0.00 % |
58 |
0.00 % |
| q20,qd2,fs60 |
18 |
0.00 % |
0 |
0.00 % |
18 |
0.00 % |
| q20,fs60 |
0 |
0.00 % |
0 |
0.00 % |
0 |
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 |
4043451 |
32.15 % |
| Transition |
G>A |
All |
909089 |
7.23 % |
| Transition |
T>C |
All |
4003058 |
31.83 % |
| Transition |
C>T |
All |
910844 |
7.24 % |
| Transversion |
A>C |
All |
229414 |
1.82 % |
| Transversion |
C>A |
All |
480854 |
3.82 % |
| Transversion |
T>G |
All |
231982 |
1.84 % |
| Transversion |
G>T |
All |
467947 |
3.72 % |
| Transversion |
A>T |
All |
442825 |
3.52 % |
| Transversion |
T>A |
All |
443921 |
3.53 % |
| Transversion |
C>G |
All |
205866 |
1.64 % |
| Transversion |
G>C |
All |
206486 |
1.64 % |
| |
|
|
|
|
| Transition |
A>G |
Passed |
632930 |
17.31 % |
| Transition |
G>A |
Passed |
589075 |
16.11 % |
| Transition |
T>C |
Passed |
634742 |
17.35 % |
| Transition |
C>T |
Passed |
592020 |
16.19 % |
| Transversion |
A>C |
Passed |
156641 |
4.28 % |
| Transversion |
C>A |
Passed |
158775 |
4.34 % |
| Transversion |
T>G |
Passed |
157168 |
4.30 % |
| Transversion |
G>T |
Passed |
158413 |
4.33 % |
| Transversion |
A>T |
Passed |
136586 |
3.73 % |
| Transversion |
T>A |
Passed |
136332 |
3.73 % |
| Transversion |
C>G |
Passed |
152192 |
4.16 % |
| Transversion |
G>C |
Passed |
152530 |
4.17 % |
| |
|
|
|
|
| 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 |
3.64 |
9866442 |
2709295 |
| Passed |
2.03 |
2448767 |
1208637 |
| dbSNPAll |
0 |
0 |
0 |
| dbSNPPassed |
0 |
0 |
0 |