/EXTERNAL BLUEPRINT/variants/K011929_K011931_K011932_K011933_K011934_5_lane_gembs
BACK
SAMPLE K011929_K011931_K011932_K011933_K011934_5_lane_gembs
Variant counts
| Type |
Total |
Pass |
% |
| SNPs |
635672460 |
214240 |
0.03 % |
| Multiallelic |
0 |
0 |
0.00 % |
VCF Filtering Stats
| Type |
#Sites |
% |
#Non-Variant Sites |
% |
#Variant Sites |
% |
| All |
635672460 |
100% |
629373008 |
99.01 % |
6299452 |
0.99 % |
| |
|
|
|
|
|
|
| Passed |
3555783 |
0.56 % |
132197 |
0.02 % |
3423586 |
96.28 % |
| Filtered |
632116677 |
99.44 % |
629240811 |
99.98 % |
2875866 |
80.88 % |
| |
|
|
|
|
|
|
| q20 |
417628878 |
66.07 % |
415493632 |
66.03 % |
2135246 |
74.25 % |
| q20,qd2 |
152661525 |
24.15 % |
152324585 |
24.21 % |
336940 |
11.72 % |
| q20,mq40 |
39855574 |
6.31 % |
39694669 |
6.31 % |
160905 |
5.60 % |
| q20,qd2,mq40 |
21735633 |
3.44 % |
21706573 |
3.45 % |
29060 |
1.01 % |
| mq40 |
230084 |
0.04 % |
16541 |
0.00 % |
213543 |
7.43 % |
| qd2 |
4429 |
0.00 % |
4376 |
0.00 % |
53 |
0.00 % |
| qd2,mq40 |
533 |
0.00 % |
435 |
0.00 % |
98 |
0.00 % |
| qd2,fs60 |
13 |
0.00 % |
0 |
0.00 % |
13 |
0.00 % |
| fs60 |
4 |
0.00 % |
0 |
0.00 % |
4 |
0.00 % |
| fs60,mq40 |
3 |
0.00 % |
0 |
0.00 % |
3 |
0.00 % |
| q20,qd2,fs60,mq40 |
1 |
0.00 % |
0 |
0.00 % |
1 |
0.00 % |
| q20,fs60 |
0 |
0.00 % |
0 |
0.00 % |
0 |
0.00 % |
| q20,qd2,fs60 |
0 |
0.00 % |
0 |
0.00 % |
0 |
0.00 % |
| q20,fs60,mq40 |
0 |
0.00 % |
0 |
0.00 % |
0 |
0.00 % |
| qd2,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 |
2505030 |
22.32 % |
| Transition |
G>A |
All |
881987 |
7.86 % |
| Transition |
T>C |
All |
3137688 |
27.96 % |
| Transition |
C>T |
All |
438265 |
3.90 % |
| Transversion |
A>C |
All |
372466 |
3.32 % |
| Transversion |
C>A |
All |
726229 |
6.47 % |
| Transversion |
T>G |
All |
442504 |
3.94 % |
| Transversion |
G>T |
All |
674038 |
6.01 % |
| Transversion |
A>T |
All |
539953 |
4.81 % |
| Transversion |
T>A |
All |
725345 |
6.46 % |
| Transversion |
C>G |
All |
352759 |
3.14 % |
| Transversion |
G>C |
All |
427502 |
3.81 % |
| |
|
|
|
|
| Transition |
A>G |
Passed |
12705 |
15.69 % |
| Transition |
G>A |
Passed |
10345 |
12.77 % |
| Transition |
T>C |
Passed |
18897 |
23.33 % |
| Transition |
C>T |
Passed |
4325 |
5.34 % |
| Transversion |
A>C |
Passed |
3640 |
4.49 % |
| Transversion |
C>A |
Passed |
5766 |
7.12 % |
| Transversion |
T>G |
Passed |
4206 |
5.19 % |
| Transversion |
G>T |
Passed |
3713 |
4.58 % |
| Transversion |
A>T |
Passed |
2266 |
2.80 % |
| Transversion |
T>A |
Passed |
5058 |
6.25 % |
| Transversion |
C>G |
Passed |
4252 |
5.25 % |
| Transversion |
G>C |
Passed |
5819 |
7.18 % |
| |
|
|
|
|
| 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 |
1.63 |
6962970 |
4260796 |
| Passed |
1.33 |
46272 |
34720 |
| dbSNPAll |
0 |
0 |
0 |
| dbSNPPassed |
0 |
0 |
0 |