/EXTERNAL BLUEPRINT/variants/K011944_K011945_K011947_3_lane_gembs
BACK
SAMPLE K011944_K011945_K011947_3_lane_gembs
Variant counts
| Type |
Total |
Pass |
% |
| SNPs |
459829841 |
45697 |
0.01 % |
| Multiallelic |
0 |
0 |
0.00 % |
VCF Filtering Stats
| Type |
#Sites |
% |
#Non-Variant Sites |
% |
#Variant Sites |
% |
| All |
459829841 |
100% |
457312017 |
99.45 % |
2517824 |
0.55 % |
| |
|
|
|
|
|
|
| Passed |
1375722 |
0.30 % |
30745 |
0.01 % |
1344977 |
97.77 % |
| Filtered |
458454119 |
99.70 % |
457281272 |
99.99 % |
1172847 |
85.25 % |
| |
|
|
|
|
|
|
| q20 |
316676924 |
69.07 % |
315768748 |
69.05 % |
908176 |
77.43 % |
| q20,qd2 |
98422360 |
21.47 % |
98310655 |
21.50 % |
111705 |
9.52 % |
| q20,mq40 |
29632245 |
6.46 % |
29566733 |
6.47 % |
65512 |
5.59 % |
| q20,qd2,mq40 |
13635051 |
2.97 % |
13624989 |
2.98 % |
10062 |
0.86 % |
| mq40 |
84618 |
0.02 % |
7311 |
0.00 % |
77307 |
6.59 % |
| qd2 |
2708 |
0.00 % |
2652 |
0.00 % |
56 |
0.00 % |
| qd2,mq40 |
206 |
0.00 % |
184 |
0.00 % |
22 |
0.00 % |
| qd2,fs60 |
3 |
0.00 % |
0 |
0.00 % |
3 |
0.00 % |
| fs60 |
2 |
0.00 % |
0 |
0.00 % |
2 |
0.00 % |
| fs60,mq40 |
2 |
0.00 % |
0 |
0.00 % |
2 |
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 % |
| 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 |
1399884 |
22.04 % |
| Transition |
G>A |
All |
501006 |
7.89 % |
| Transition |
T>C |
All |
1769085 |
27.85 % |
| Transition |
C>T |
All |
252229 |
3.97 % |
| Transversion |
A>C |
All |
225552 |
3.55 % |
| Transversion |
C>A |
All |
404820 |
6.37 % |
| Transversion |
T>G |
All |
263145 |
4.14 % |
| Transversion |
G>T |
All |
371473 |
5.85 % |
| Transversion |
A>T |
All |
294305 |
4.63 % |
| Transversion |
T>A |
All |
410067 |
6.46 % |
| Transversion |
C>G |
All |
208455 |
3.28 % |
| Transversion |
G>C |
All |
251956 |
3.97 % |
| |
|
|
|
|
| Transition |
A>G |
Passed |
2284 |
15.41 % |
| Transition |
G>A |
Passed |
1896 |
12.79 % |
| Transition |
T>C |
Passed |
3244 |
21.89 % |
| Transition |
C>T |
Passed |
986 |
6.65 % |
| Transversion |
A>C |
Passed |
598 |
4.03 % |
| Transversion |
C>A |
Passed |
925 |
6.24 % |
| Transversion |
T>G |
Passed |
801 |
5.40 % |
| Transversion |
G>T |
Passed |
741 |
5.00 % |
| Transversion |
A>T |
Passed |
418 |
2.82 % |
| Transversion |
T>A |
Passed |
848 |
5.72 % |
| Transversion |
C>G |
Passed |
959 |
6.47 % |
| Transversion |
G>C |
Passed |
1121 |
7.56 % |
| |
|
|
|
|
| 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 |
1.61 |
3922204 |
2429773 |
| Passed |
1.31 |
8410 |
6411 |
| dbSNPAll |
0 |
0 |
0 |
| dbSNPPassed |
0 |
0 |
0 |