/EXTERNAL BLUEPRINT/variants/K006313_21_lane_gembs
BACK
SAMPLE K006313_21_lane_gembs
Variant counts
| Type |
Total |
Pass |
% |
| SNPs |
1054450149 |
510507800 |
48.41 % |
| Multiallelic |
0 |
0 |
0.00 % |
VCF Filtering Stats
| Type |
#Sites |
% |
#Non-Variant Sites |
% |
#Variant Sites |
% |
| All |
1054450149 |
100% |
1037445759 |
98.39 % |
17004390 |
1.61 % |
| |
|
|
|
|
|
|
| Passed |
512091428 |
48.56 % |
509509408 |
49.11 % |
2582020 |
0.50 % |
| Filtered |
542358721 |
51.44 % |
527936351 |
50.89 % |
14422370 |
2.82 % |
| |
|
|
|
|
|
|
| q20 |
444103854 |
81.88 % |
442296474 |
83.78 % |
1807380 |
12.53 % |
| q20,qd2 |
65161495 |
12.01 % |
53031170 |
10.04 % |
12130325 |
84.11 % |
| q20,mq40 |
15043999 |
2.77 % |
14959325 |
2.83 % |
84674 |
0.59 % |
| qd2 |
7689430 |
1.42 % |
7605217 |
1.44 % |
84213 |
0.58 % |
| mq40 |
6901205 |
1.27 % |
6756066 |
1.28 % |
145139 |
1.01 % |
| q20,qd2,mq40 |
3355224 |
0.62 % |
3209465 |
0.61 % |
145759 |
1.01 % |
| qd2,mq40 |
90944 |
0.02 % |
78634 |
0.01 % |
12310 |
0.09 % |
| q20,qd2,fs60 |
3451 |
0.00 % |
0 |
0.00 % |
3451 |
0.02 % |
| qd2,fs60 |
3008 |
0.00 % |
0 |
0.00 % |
3008 |
0.02 % |
| qd2,fs60,mq40 |
2284 |
0.00 % |
0 |
0.00 % |
2284 |
0.02 % |
| fs60 |
2162 |
0.00 % |
0 |
0.00 % |
2162 |
0.01 % |
| q20,qd2,fs60,mq40 |
940 |
0.00 % |
0 |
0.00 % |
940 |
0.01 % |
| fs60,mq40 |
722 |
0.00 % |
0 |
0.00 % |
722 |
0.01 % |
| q20,fs60,mq40 |
2 |
0.00 % |
0 |
0.00 % |
2 |
0.00 % |
| q20,fs60 |
1 |
0.00 % |
0 |
0.00 % |
1 |
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 |
2892100 |
10.39 % |
| Transition |
G>A |
All |
10004904 |
35.96 % |
| Transition |
T>C |
All |
2603985 |
9.36 % |
| Transition |
C>T |
All |
9865163 |
35.45 % |
| Transversion |
A>C |
All |
209470 |
0.75 % |
| Transversion |
C>A |
All |
476109 |
1.71 % |
| Transversion |
T>G |
All |
235589 |
0.85 % |
| Transversion |
G>T |
All |
455385 |
1.64 % |
| Transversion |
A>T |
All |
350426 |
1.26 % |
| Transversion |
T>A |
All |
363110 |
1.30 % |
| Transversion |
C>G |
All |
192298 |
0.69 % |
| Transversion |
G>C |
All |
176733 |
0.64 % |
| |
|
|
|
|
| Transition |
A>G |
Passed |
293339 |
19.71 % |
| Transition |
G>A |
Passed |
255524 |
17.17 % |
| Transition |
T>C |
Passed |
292400 |
19.64 % |
| Transition |
C>T |
Passed |
255314 |
17.15 % |
| Transversion |
A>C |
Passed |
51920 |
3.49 % |
| Transversion |
C>A |
Passed |
46305 |
3.11 % |
| Transversion |
T>G |
Passed |
51922 |
3.49 % |
| Transversion |
G>T |
Passed |
46187 |
3.10 % |
| Transversion |
A>T |
Passed |
29144 |
1.96 % |
| Transversion |
T>A |
Passed |
28713 |
1.93 % |
| Transversion |
C>G |
Passed |
68814 |
4.62 % |
| Transversion |
G>C |
Passed |
68865 |
4.63 % |
| |
|
|
|
|
| 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 |
10.32 |
25366152 |
2459120 |
| Passed |
2.80 |
1096577 |
391870 |
| dbSNPAll |
0 |
0 |
0 |
| dbSNPPassed |
0 |
0 |
0 |