/EXTERNAL BLUEPRINT/variants/K006266_8_lane_gembs
BACK
SAMPLE K006266_8_lane_gembs
Variant counts
| Type |
Total |
Pass |
% |
| SNPs |
1153821309 |
894484773 |
77.52 % |
| Multiallelic |
0 |
0 |
0.00 % |
VCF Filtering Stats
| Type |
#Sites |
% |
#Non-Variant Sites |
% |
#Variant Sites |
% |
| All |
1153821309 |
100% |
1134689868 |
98.34 % |
19131441 |
1.66 % |
| |
|
|
|
|
|
|
| Passed |
896166895 |
77.67 % |
892609535 |
78.67 % |
3557360 |
0.40 % |
| Filtered |
257654414 |
22.33 % |
242080333 |
21.33 % |
15574081 |
1.74 % |
| |
|
|
|
|
|
|
| q20 |
201920545 |
78.37 % |
199373099 |
82.36 % |
2547446 |
16.36 % |
| q20,qd2 |
27576245 |
10.70 % |
15319174 |
6.33 % |
12257071 |
78.70 % |
| q20,mq40 |
12236463 |
4.75 % |
12112432 |
5.00 % |
124031 |
0.80 % |
| mq40 |
8540503 |
3.31 % |
8313959 |
3.43 % |
226544 |
1.45 % |
| qd2 |
4504689 |
1.75 % |
4333601 |
1.79 % |
171088 |
1.10 % |
| q20,qd2,mq40 |
2731781 |
1.06 % |
2517691 |
1.04 % |
214090 |
1.37 % |
| qd2,mq40 |
127980 |
0.05 % |
110377 |
0.05 % |
17603 |
0.11 % |
| q20,qd2,fs60 |
6524 |
0.00 % |
0 |
0.00 % |
6524 |
0.04 % |
| fs60 |
3266 |
0.00 % |
0 |
0.00 % |
3266 |
0.02 % |
| qd2,fs60 |
2436 |
0.00 % |
0 |
0.00 % |
2436 |
0.02 % |
| qd2,fs60,mq40 |
2306 |
0.00 % |
0 |
0.00 % |
2306 |
0.01 % |
| fs60,mq40 |
988 |
0.00 % |
0 |
0.00 % |
988 |
0.01 % |
| q20,qd2,fs60,mq40 |
673 |
0.00 % |
0 |
0.00 % |
673 |
0.00 % |
| q20,fs60,mq40 |
8 |
0.00 % |
0 |
0.00 % |
8 |
0.00 % |
| q20,fs60 |
7 |
0.00 % |
0 |
0.00 % |
7 |
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 |
4137329 |
14.90 % |
| Transition |
G>A |
All |
8491031 |
30.57 % |
| Transition |
T>C |
All |
4055237 |
14.60 % |
| Transition |
C>T |
All |
8461566 |
30.46 % |
| Transversion |
A>C |
All |
212798 |
0.77 % |
| Transversion |
C>A |
All |
443519 |
1.60 % |
| Transversion |
T>G |
All |
220735 |
0.79 % |
| Transversion |
G>T |
All |
434105 |
1.56 % |
| Transversion |
A>T |
All |
460505 |
1.66 % |
| Transversion |
T>A |
All |
459678 |
1.65 % |
| Transversion |
C>G |
All |
202166 |
0.73 % |
| Transversion |
G>C |
All |
197925 |
0.71 % |
| |
|
|
|
|
| Transition |
A>G |
Passed |
528909 |
18.45 % |
| Transition |
G>A |
Passed |
477206 |
16.65 % |
| Transition |
T>C |
Passed |
527555 |
18.40 % |
| Transition |
C>T |
Passed |
478651 |
16.70 % |
| Transversion |
A>C |
Passed |
112457 |
3.92 % |
| Transversion |
C>A |
Passed |
107640 |
3.76 % |
| Transversion |
T>G |
Passed |
112399 |
3.92 % |
| Transversion |
G>T |
Passed |
107420 |
3.75 % |
| Transversion |
A>T |
Passed |
84895 |
2.96 % |
| Transversion |
T>A |
Passed |
85010 |
2.97 % |
| Transversion |
C>G |
Passed |
121950 |
4.25 % |
| Transversion |
G>C |
Passed |
122425 |
4.27 % |
| |
|
|
|
|
| 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 |
9.56 |
25145163 |
2631431 |
| Passed |
2.36 |
2012321 |
854196 |
| dbSNPAll |
0 |
0 |
0 |
| dbSNPPassed |
0 |
0 |
0 |