/EXTERNAL BLUEPRINT/variants/K006275_11_lane_gembs
BACK
SAMPLE K006275_11_lane_gembs
Variant counts
| Type |
Total |
Pass |
% |
| SNPs |
1124789070 |
680513180 |
60.50 % |
| Multiallelic |
0 |
0 |
0.00 % |
VCF Filtering Stats
| Type |
#Sites |
% |
#Non-Variant Sites |
% |
#Variant Sites |
% |
| All |
1124789070 |
100% |
1110736424 |
98.75 % |
14052646 |
1.25 % |
| |
|
|
|
|
|
|
| Passed |
682612013 |
60.69 % |
678919600 |
61.12 % |
3692413 |
0.54 % |
| Filtered |
442177057 |
39.31 % |
431816824 |
38.88 % |
10360233 |
1.52 % |
| |
|
|
|
|
|
|
| q20 |
379801076 |
85.89 % |
378035343 |
87.55 % |
1765733 |
17.04 % |
| q20,qd2 |
35846691 |
8.11 % |
27844334 |
6.45 % |
8002357 |
77.24 % |
| q20,mq40 |
14592648 |
3.30 % |
14485981 |
3.35 % |
106667 |
1.03 % |
| mq40 |
6200749 |
1.40 % |
6013381 |
1.39 % |
187368 |
1.81 % |
| q20,qd2,mq40 |
3205594 |
0.72 % |
3020935 |
0.70 % |
184659 |
1.78 % |
| qd2 |
2460091 |
0.56 % |
2359678 |
0.55 % |
100413 |
0.97 % |
| qd2,mq40 |
66346 |
0.02 % |
57172 |
0.01 % |
9174 |
0.09 % |
| q20,qd2,fs60 |
894 |
0.00 % |
0 |
0.00 % |
894 |
0.01 % |
| qd2,fs60,mq40 |
875 |
0.00 % |
0 |
0.00 % |
875 |
0.01 % |
| fs60 |
817 |
0.00 % |
0 |
0.00 % |
817 |
0.01 % |
| qd2,fs60 |
457 |
0.00 % |
0 |
0.00 % |
457 |
0.00 % |
| fs60,mq40 |
424 |
0.00 % |
0 |
0.00 % |
424 |
0.00 % |
| q20,qd2,fs60,mq40 |
393 |
0.00 % |
0 |
0.00 % |
393 |
0.00 % |
| q20,fs60,mq40 |
2 |
0.00 % |
0 |
0.00 % |
2 |
0.00 % |
| q20,fs60 |
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 |
3718394 |
23.42 % |
| Transition |
G>A |
All |
2807400 |
17.68 % |
| Transition |
T>C |
All |
3594629 |
22.64 % |
| Transition |
C>T |
All |
2681048 |
16.89 % |
| Transversion |
A>C |
All |
230830 |
1.45 % |
| Transversion |
C>A |
All |
625137 |
3.94 % |
| Transversion |
T>G |
All |
241411 |
1.52 % |
| Transversion |
G>T |
All |
606181 |
3.82 % |
| Transversion |
A>T |
All |
481761 |
3.03 % |
| Transversion |
T>A |
All |
477481 |
3.01 % |
| Transversion |
C>G |
All |
209176 |
1.32 % |
| Transversion |
G>C |
All |
201868 |
1.27 % |
| |
|
|
|
|
| Transition |
A>G |
Passed |
428176 |
18.96 % |
| Transition |
G>A |
Passed |
378836 |
16.78 % |
| Transition |
T>C |
Passed |
425793 |
18.86 % |
| Transition |
C>T |
Passed |
378006 |
16.74 % |
| Transversion |
A>C |
Passed |
85056 |
3.77 % |
| Transversion |
C>A |
Passed |
80995 |
3.59 % |
| Transversion |
T>G |
Passed |
84517 |
3.74 % |
| Transversion |
G>T |
Passed |
80348 |
3.56 % |
| Transversion |
A>T |
Passed |
57660 |
2.55 % |
| Transversion |
T>A |
Passed |
58031 |
2.57 % |
| Transversion |
C>G |
Passed |
100088 |
4.43 % |
| Transversion |
G>C |
Passed |
100698 |
4.46 % |
| |
|
|
|
|
| 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 |
4.16 |
12801471 |
3073845 |
| Passed |
2.49 |
1610811 |
647393 |
| dbSNPAll |
0 |
0 |
0 |
| dbSNPPassed |
0 |
0 |
0 |