/EXTERNAL BLUEPRINT/variants/K006394_K006407_19_lane_gembs
BACK
SAMPLE K006394_K006407_19_lane_gembs
Variant counts
| Type |
Total |
Pass |
% |
| SNPs |
1158590255 |
1013626861 |
87.49 % |
| Multiallelic |
0 |
0 |
0.00 % |
VCF Filtering Stats
| Type |
#Sites |
% |
#Non-Variant Sites |
% |
#Variant Sites |
% |
| All |
1158590255 |
100% |
1146966905 |
99.00 % |
11623350 |
1.00 % |
| |
|
|
|
|
|
|
| Passed |
1014908618 |
87.60 % |
1011328989 |
88.17 % |
3579629 |
0.35 % |
| Filtered |
143681637 |
12.40 % |
135637916 |
11.83 % |
8043721 |
0.79 % |
| |
|
|
|
|
|
|
| q20 |
103314650 |
71.91 % |
102336544 |
75.45 % |
978106 |
12.16 % |
| q20,mq40 |
11707930 |
8.15 % |
11608378 |
8.56 % |
99552 |
1.24 % |
| q20,qd2 |
9857853 |
6.86 % |
3451977 |
2.54 % |
6405876 |
79.64 % |
| qd2 |
8902351 |
6.20 % |
8745934 |
6.45 % |
156417 |
1.94 % |
| mq40 |
6963995 |
4.85 % |
6766074 |
4.99 % |
197921 |
2.46 % |
| q20,qd2,mq40 |
2810616 |
1.96 % |
2634978 |
1.94 % |
175638 |
2.18 % |
| qd2,mq40 |
109675 |
0.08 % |
94031 |
0.07 % |
15644 |
0.19 % |
| fs60 |
4086 |
0.00 % |
0 |
0.00 % |
4086 |
0.05 % |
| qd2,fs60 |
3997 |
0.00 % |
0 |
0.00 % |
3997 |
0.05 % |
| q20,qd2,fs60 |
2754 |
0.00 % |
0 |
0.00 % |
2754 |
0.03 % |
| qd2,fs60,mq40 |
2454 |
0.00 % |
0 |
0.00 % |
2454 |
0.03 % |
| fs60,mq40 |
891 |
0.00 % |
0 |
0.00 % |
891 |
0.01 % |
| q20,qd2,fs60,mq40 |
378 |
0.00 % |
0 |
0.00 % |
378 |
0.00 % |
| q20,fs60,mq40 |
5 |
0.00 % |
0 |
0.00 % |
5 |
0.00 % |
| q20,fs60 |
2 |
0.00 % |
0 |
0.00 % |
2 |
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 |
4436616 |
32.93 % |
| Transition |
G>A |
All |
1080154 |
8.02 % |
| Transition |
T>C |
All |
4403467 |
32.69 % |
| Transition |
C>T |
All |
1081119 |
8.03 % |
| Transversion |
A>C |
All |
218557 |
1.62 % |
| Transversion |
C>A |
All |
453725 |
3.37 % |
| Transversion |
T>G |
All |
221507 |
1.64 % |
| Transversion |
G>T |
All |
447532 |
3.32 % |
| Transversion |
A>T |
All |
364827 |
2.71 % |
| Transversion |
T>A |
All |
360981 |
2.68 % |
| Transversion |
C>G |
All |
201696 |
1.50 % |
| Transversion |
G>C |
All |
201155 |
1.49 % |
| |
|
|
|
|
| Transition |
A>G |
Passed |
601059 |
17.44 % |
| Transition |
G>A |
Passed |
558730 |
16.21 % |
| Transition |
T>C |
Passed |
603457 |
17.51 % |
| Transition |
C>T |
Passed |
562085 |
16.31 % |
| Transversion |
A>C |
Passed |
147337 |
4.27 % |
| Transversion |
C>A |
Passed |
144595 |
4.20 % |
| Transversion |
T>G |
Passed |
147564 |
4.28 % |
| Transversion |
G>T |
Passed |
144422 |
4.19 % |
| Transversion |
A>T |
Passed |
123234 |
3.58 % |
| Transversion |
T>A |
Passed |
123475 |
3.58 % |
| Transversion |
C>G |
Passed |
144890 |
4.20 % |
| Transversion |
G>C |
Passed |
145952 |
4.23 % |
| |
|
|
|
|
| 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 |
4.45 |
11001356 |
2469980 |
| Passed |
2.07 |
2325331 |
1121469 |
| dbSNPAll |
0 |
0 |
0 |
| dbSNPPassed |
0 |
0 |
0 |