/EXTERNAL BLUEPRINT/variants/K012130_1_lane_gembs
BACK
SAMPLE K012130_1_lane_gembs
Variant counts
| Type |
Total |
Pass |
% |
| SNPs |
775936659 |
1874150 |
0.24 % |
| Multiallelic |
0 |
0 |
0.00 % |
VCF Filtering Stats
| Type |
#Sites |
% |
#Non-Variant Sites |
% |
#Variant Sites |
% |
| All |
775936659 |
100% |
764011773 |
98.46 % |
11924886 |
1.54 % |
| |
|
|
|
|
|
|
| Passed |
7893334 |
1.02 % |
1647688 |
0.22 % |
6245646 |
79.13 % |
| Filtered |
768043325 |
98.98 % |
762364085 |
99.78 % |
5679240 |
71.95 % |
| |
|
|
|
|
|
|
| q20 |
536259938 |
69.82 % |
531916605 |
69.77 % |
4343333 |
76.48 % |
| q20,qd2 |
167454106 |
21.80 % |
166765618 |
21.87 % |
688488 |
12.12 % |
| q20,mq40 |
42227213 |
5.50 % |
41965562 |
5.50 % |
261651 |
4.61 % |
| q20,qd2,mq40 |
21708226 |
2.83 % |
21663306 |
2.84 % |
44920 |
0.79 % |
| mq40 |
388504 |
0.05 % |
47938 |
0.01 % |
340566 |
6.00 % |
| qd2 |
4319 |
0.00 % |
4231 |
0.00 % |
88 |
0.00 % |
| qd2,mq40 |
982 |
0.00 % |
825 |
0.00 % |
157 |
0.00 % |
| qd2,fs60 |
12 |
0.00 % |
0 |
0.00 % |
12 |
0.00 % |
| fs60 |
7 |
0.00 % |
0 |
0.00 % |
7 |
0.00 % |
| fs60,mq40 |
7 |
0.00 % |
0 |
0.00 % |
7 |
0.00 % |
| qd2,fs60,mq40 |
5 |
0.00 % |
0 |
0.00 % |
5 |
0.00 % |
| q20,qd2,fs60,mq40 |
5 |
0.00 % |
0 |
0.00 % |
5 |
0.00 % |
| q20,qd2,fs60 |
1 |
0.00 % |
0 |
0.00 % |
1 |
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 |
3817331 |
23.31 % |
| Transition |
G>A |
All |
1314161 |
8.02 % |
| Transition |
T>C |
All |
4917103 |
30.02 % |
| Transition |
C>T |
All |
625740 |
3.82 % |
| Transversion |
A>C |
All |
593279 |
3.62 % |
| Transversion |
C>A |
All |
888106 |
5.42 % |
| Transversion |
T>G |
All |
733067 |
4.48 % |
| Transversion |
G>T |
All |
794355 |
4.85 % |
| Transversion |
A>T |
All |
647301 |
3.95 % |
| Transversion |
T>A |
All |
898686 |
5.49 % |
| Transversion |
C>G |
All |
530615 |
3.24 % |
| Transversion |
G>C |
All |
619345 |
3.78 % |
| |
|
|
|
|
| Transition |
A>G |
Passed |
34917 |
15.68 % |
| Transition |
G>A |
Passed |
32671 |
14.67 % |
| Transition |
T>C |
Passed |
63522 |
28.53 % |
| Transition |
C>T |
Passed |
14201 |
6.38 % |
| Transversion |
A>C |
Passed |
9352 |
4.20 % |
| Transversion |
C>A |
Passed |
12404 |
5.57 % |
| Transversion |
T>G |
Passed |
9356 |
4.20 % |
| Transversion |
G>T |
Passed |
6875 |
3.09 % |
| Transversion |
A>T |
Passed |
4491 |
2.02 % |
| Transversion |
T>A |
Passed |
10804 |
4.85 % |
| Transversion |
C>G |
Passed |
9642 |
4.33 % |
| Transversion |
G>C |
Passed |
14437 |
6.48 % |
| |
|
|
|
|
| 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 |
1.87 |
10674335 |
5704754 |
| Passed |
1.88 |
145311 |
77361 |
| dbSNPAll |
0 |
0 |
0 |
| dbSNPPassed |
0 |
0 |
0 |