/EXTERNAL BLUEPRINT/variants/K011972_K011976_K012000_K012001_4_lane_gembs
BACK
SAMPLE K011972_K011976_K012000_K012001_4_lane_gembs
Variant counts
| Type |
Total |
Pass |
% |
| SNPs |
836316891 |
1451537 |
0.17 % |
| Multiallelic |
0 |
0 |
0.00 % |
VCF Filtering Stats
| Type |
#Sites |
% |
#Non-Variant Sites |
% |
#Variant Sites |
% |
| All |
836316891 |
100% |
822181031 |
98.31 % |
14135860 |
1.69 % |
| |
|
|
|
|
|
|
| Passed |
9354232 |
1.12 % |
1215223 |
0.15 % |
8139009 |
87.01 % |
| Filtered |
826962659 |
98.88 % |
820965808 |
99.85 % |
5996851 |
64.11 % |
| |
|
|
|
|
|
|
| q20 |
620188406 |
75.00 % |
615869058 |
75.02 % |
4319348 |
72.03 % |
| q20,qd2 |
132610261 |
16.04 % |
131715739 |
16.04 % |
894522 |
14.92 % |
| q20,mq40 |
52208182 |
6.31 % |
51919273 |
6.32 % |
288909 |
4.82 % |
| q20,qd2,mq40 |
21467338 |
2.60 % |
21410828 |
2.61 % |
56510 |
0.94 % |
| mq40 |
482472 |
0.06 % |
45251 |
0.01 % |
437221 |
7.29 % |
| qd2 |
5043 |
0.00 % |
4935 |
0.00 % |
108 |
0.00 % |
| qd2,mq40 |
912 |
0.00 % |
724 |
0.00 % |
188 |
0.00 % |
| fs60,mq40 |
18 |
0.00 % |
0 |
0.00 % |
18 |
0.00 % |
| fs60 |
10 |
0.00 % |
0 |
0.00 % |
10 |
0.00 % |
| qd2,fs60 |
9 |
0.00 % |
0 |
0.00 % |
9 |
0.00 % |
| qd2,fs60,mq40 |
4 |
0.00 % |
0 |
0.00 % |
4 |
0.00 % |
| q20,qd2,fs60,mq40 |
3 |
0.00 % |
0 |
0.00 % |
3 |
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 |
4263150 |
22.21 % |
| Transition |
G>A |
All |
1510759 |
7.87 % |
| Transition |
T>C |
All |
5431059 |
28.29 % |
| Transition |
C>T |
All |
734421 |
3.83 % |
| Transversion |
A>C |
All |
678164 |
3.53 % |
| Transversion |
C>A |
All |
1200251 |
6.25 % |
| Transversion |
T>G |
All |
770387 |
4.01 % |
| Transversion |
G>T |
All |
1097568 |
5.72 % |
| Transversion |
A>T |
All |
932452 |
4.86 % |
| Transversion |
T>A |
All |
1251663 |
6.52 % |
| Transversion |
C>G |
All |
598993 |
3.12 % |
| Transversion |
G>C |
All |
727161 |
3.79 % |
| |
|
|
|
|
| Transition |
A>G |
Passed |
35540 |
15.20 % |
| Transition |
G>A |
Passed |
30783 |
13.17 % |
| Transition |
T>C |
Passed |
60126 |
25.71 % |
| Transition |
C>T |
Passed |
14943 |
6.39 % |
| Transversion |
A>C |
Passed |
11238 |
4.81 % |
| Transversion |
C>A |
Passed |
13689 |
5.85 % |
| Transversion |
T>G |
Passed |
11101 |
4.75 % |
| Transversion |
G>T |
Passed |
9167 |
3.92 % |
| Transversion |
A>T |
Passed |
6323 |
2.70 % |
| Transversion |
T>A |
Passed |
13460 |
5.76 % |
| Transversion |
C>G |
Passed |
11535 |
4.93 % |
| Transversion |
G>C |
Passed |
15912 |
6.81 % |
| |
|
|
|
|
| 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 |
1.65 |
11939389 |
7256639 |
| Passed |
1.53 |
141392 |
92425 |
| dbSNPAll |
0 |
0 |
0 |
| dbSNPPassed |
0 |
0 |
0 |