/EXTERNAL BLUEPRINT/variants/K006343_12_lane_gembs
BACK
SAMPLE K006343_12_lane_gembs
Variant counts
| Type |
Total |
Pass |
% |
| SNPs |
1047150933 |
495364760 |
47.31 % |
| Multiallelic |
0 |
0 |
0.00 % |
VCF Filtering Stats
| Type |
#Sites |
% |
#Non-Variant Sites |
% |
#Variant Sites |
% |
| All |
1047150933 |
100% |
1029541104 |
98.32 % |
17609829 |
1.68 % |
| |
|
|
|
|
|
|
| Passed |
496885567 |
47.45 % |
494389265 |
48.02 % |
2496302 |
0.50 % |
| Filtered |
550265366 |
52.55 % |
535151839 |
51.98 % |
15113527 |
3.04 % |
| |
|
|
|
|
|
|
| q20 |
449116670 |
81.62 % |
447478565 |
83.62 % |
1638105 |
10.84 % |
| q20,qd2 |
70186197 |
12.75 % |
57243188 |
10.70 % |
12943009 |
85.64 % |
| q20,mq40 |
16314463 |
2.96 % |
16209827 |
3.03 % |
104636 |
0.69 % |
| mq40 |
6384764 |
1.16 % |
6239940 |
1.17 % |
144824 |
0.96 % |
| qd2 |
4319552 |
0.78 % |
4242502 |
0.79 % |
77050 |
0.51 % |
| q20,qd2,mq40 |
3843265 |
0.70 % |
3660440 |
0.68 % |
182825 |
1.21 % |
| qd2,mq40 |
88695 |
0.02 % |
77377 |
0.01 % |
11318 |
0.07 % |
| q20,qd2,fs60 |
3818 |
0.00 % |
0 |
0.00 % |
3818 |
0.03 % |
| fs60 |
2346 |
0.00 % |
0 |
0.00 % |
2346 |
0.02 % |
| qd2,fs60 |
2298 |
0.00 % |
0 |
0.00 % |
2298 |
0.02 % |
| qd2,fs60,mq40 |
1859 |
0.00 % |
0 |
0.00 % |
1859 |
0.01 % |
| q20,qd2,fs60,mq40 |
800 |
0.00 % |
0 |
0.00 % |
800 |
0.01 % |
| fs60,mq40 |
636 |
0.00 % |
0 |
0.00 % |
636 |
0.00 % |
| q20,fs60 |
3 |
0.00 % |
0 |
0.00 % |
3 |
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 |
2722323 |
10.28 % |
| Transition |
G>A |
All |
9315115 |
35.17 % |
| Transition |
T>C |
All |
2500617 |
9.44 % |
| Transition |
C>T |
All |
9140812 |
34.51 % |
| Transversion |
A>C |
All |
202408 |
0.76 % |
| Transversion |
C>A |
All |
605288 |
2.29 % |
| Transversion |
T>G |
All |
224630 |
0.85 % |
| Transversion |
G>T |
All |
593831 |
2.24 % |
| Transversion |
A>T |
All |
409128 |
1.54 % |
| Transversion |
T>A |
All |
411880 |
1.56 % |
| Transversion |
C>G |
All |
186433 |
0.70 % |
| Transversion |
G>C |
All |
172758 |
0.65 % |
| |
|
|
|
|
| Transition |
A>G |
Passed |
283779 |
19.37 % |
| Transition |
G>A |
Passed |
257172 |
17.56 % |
| Transition |
T>C |
Passed |
282463 |
19.29 % |
| Transition |
C>T |
Passed |
257278 |
17.57 % |
| Transversion |
A>C |
Passed |
51725 |
3.53 % |
| Transversion |
C>A |
Passed |
45624 |
3.11 % |
| Transversion |
T>G |
Passed |
51241 |
3.50 % |
| Transversion |
G>T |
Passed |
45716 |
3.12 % |
| Transversion |
A>T |
Passed |
28251 |
1.93 % |
| Transversion |
T>A |
Passed |
28143 |
1.92 % |
| Transversion |
C>G |
Passed |
66398 |
4.53 % |
| Transversion |
G>C |
Passed |
66884 |
4.57 % |
| |
|
|
|
|
| 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 |
8.44 |
23678867 |
2806356 |
| Passed |
2.81 |
1080692 |
383982 |
| dbSNPAll |
0 |
0 |
0 |
| dbSNPPassed |
0 |
0 |
0 |