/EXTERNAL BLUEPRINT/variants/K011721_1_lane_gembs
BACK
SAMPLE K011721_1_lane_gembs
Variant counts
| Type |
Total |
Pass |
% |
| SNPs |
503241799 |
52659 |
0.01 % |
| Multiallelic |
0 |
0 |
0.00 % |
VCF Filtering Stats
| Type |
#Sites |
% |
#Non-Variant Sites |
% |
#Variant Sites |
% |
| All |
503241799 |
100% |
499311989 |
99.22 % |
3929810 |
0.78 % |
| |
|
|
|
|
|
|
| Passed |
1783449 |
0.35 % |
31978 |
0.01 % |
1751471 |
98.21 % |
| Filtered |
501458350 |
99.65 % |
499280011 |
99.99 % |
2178339 |
122.14 % |
| |
|
|
|
|
|
|
| q20 |
301283772 |
60.08 % |
299485055 |
59.98 % |
1798717 |
82.57 % |
| q20,qd2 |
149249392 |
29.76 % |
149121563 |
29.87 % |
127829 |
5.87 % |
| q20,mq40 |
30932619 |
6.17 % |
30802157 |
6.17 % |
130462 |
5.99 % |
| q20,qd2,mq40 |
19871460 |
3.96 % |
19859309 |
3.98 % |
12151 |
0.56 % |
| mq40 |
117328 |
0.02 % |
8239 |
0.00 % |
109089 |
5.01 % |
| qd2 |
3518 |
0.00 % |
3493 |
0.00 % |
25 |
0.00 % |
| qd2,mq40 |
237 |
0.00 % |
195 |
0.00 % |
42 |
0.00 % |
| qd2,fs60 |
14 |
0.00 % |
0 |
0.00 % |
14 |
0.00 % |
| fs60 |
8 |
0.00 % |
0 |
0.00 % |
8 |
0.00 % |
| fs60,mq40 |
1 |
0.00 % |
0 |
0.00 % |
1 |
0.00 % |
| 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 % |
| q20,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 |
1926071 |
23.18 % |
| Transition |
G>A |
All |
598154 |
7.20 % |
| Transition |
T>C |
All |
2456207 |
29.56 % |
| Transition |
C>T |
All |
291780 |
3.51 % |
| Transversion |
A>C |
All |
411094 |
4.95 % |
| Transversion |
C>A |
All |
393447 |
4.74 % |
| Transversion |
T>G |
All |
498635 |
6.00 % |
| Transversion |
G>T |
All |
353036 |
4.25 % |
| Transversion |
A>T |
All |
303387 |
3.65 % |
| Transversion |
T>A |
All |
423827 |
5.10 % |
| Transversion |
C>G |
All |
310733 |
3.74 % |
| Transversion |
G>C |
All |
342290 |
4.12 % |
| |
|
|
|
|
| Transition |
A>G |
Passed |
3011 |
14.86 % |
| Transition |
G>A |
Passed |
3228 |
15.93 % |
| Transition |
T>C |
Passed |
4872 |
24.04 % |
| Transition |
C>T |
Passed |
1389 |
6.85 % |
| Transversion |
A>C |
Passed |
950 |
4.69 % |
| Transversion |
C>A |
Passed |
1154 |
5.69 % |
| Transversion |
T>G |
Passed |
1009 |
4.98 % |
| Transversion |
G>T |
Passed |
644 |
3.18 % |
| Transversion |
A>T |
Passed |
441 |
2.18 % |
| Transversion |
T>A |
Passed |
994 |
4.91 % |
| Transversion |
C>G |
Passed |
1043 |
5.15 % |
| Transversion |
G>C |
Passed |
1529 |
7.55 % |
| |
|
|
|
|
| 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 |
1.74 |
5272212 |
3036449 |
| Passed |
1.61 |
12500 |
7764 |
| dbSNPAll |
0 |
0 |
0 |
| dbSNPPassed |
0 |
0 |
0 |