/EXTERNAL BLUEPRINT/variants/K006283_14_lane_gembs
BACK
SAMPLE K006283_14_lane_gembs
Variant counts
| Type |
Total |
Pass |
% |
| SNPs |
1115784355 |
565357740 |
50.67 % |
| Multiallelic |
0 |
0 |
0.00 % |
VCF Filtering Stats
| Type |
#Sites |
% |
#Non-Variant Sites |
% |
#Variant Sites |
% |
| All |
1115784355 |
100% |
1103863484 |
98.93 % |
11920871 |
1.07 % |
| |
|
|
|
|
|
|
| Passed |
567718242 |
50.88 % |
564103171 |
51.10 % |
3615071 |
0.64 % |
| Filtered |
548066113 |
49.12 % |
539760313 |
48.90 % |
8305800 |
1.46 % |
| |
|
|
|
|
|
|
| q20 |
490707088 |
89.53 % |
488866587 |
90.57 % |
1840501 |
22.16 % |
| q20,qd2 |
31246774 |
5.70 % |
25310690 |
4.69 % |
5936084 |
71.47 % |
| q20,mq40 |
15388332 |
2.81 % |
15294712 |
2.83 % |
93620 |
1.13 % |
| mq40 |
5721149 |
1.04 % |
5554148 |
1.03 % |
167001 |
2.01 % |
| q20,qd2,mq40 |
2913910 |
0.53 % |
2767211 |
0.51 % |
146699 |
1.77 % |
| qd2 |
2002781 |
0.37 % |
1899751 |
0.35 % |
103030 |
1.24 % |
| qd2,mq40 |
78659 |
0.01 % |
67214 |
0.01 % |
11445 |
0.14 % |
| fs60 |
1657 |
0.00 % |
0 |
0.00 % |
1657 |
0.02 % |
| q20,qd2,fs60 |
1636 |
0.00 % |
0 |
0.00 % |
1636 |
0.02 % |
| qd2,fs60 |
1575 |
0.00 % |
0 |
0.00 % |
1575 |
0.02 % |
| qd2,fs60,mq40 |
1532 |
0.00 % |
0 |
0.00 % |
1532 |
0.02 % |
| fs60,mq40 |
615 |
0.00 % |
0 |
0.00 % |
615 |
0.01 % |
| q20,qd2,fs60,mq40 |
400 |
0.00 % |
0 |
0.00 % |
400 |
0.00 % |
| q20,fs60 |
3 |
0.00 % |
0 |
0.00 % |
3 |
0.00 % |
| q20,fs60,mq40 |
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 |
3664901 |
24.97 % |
| Transition |
G>A |
All |
2382012 |
16.23 % |
| Transition |
T>C |
All |
3525594 |
24.02 % |
| Transition |
C>T |
All |
2364537 |
16.11 % |
| Transversion |
A>C |
All |
214675 |
1.46 % |
| Transversion |
C>A |
All |
568838 |
3.88 % |
| Transversion |
T>G |
All |
225716 |
1.54 % |
| Transversion |
G>T |
All |
551565 |
3.76 % |
| Transversion |
A>T |
All |
382630 |
2.61 % |
| Transversion |
T>A |
All |
379379 |
2.58 % |
| Transversion |
C>G |
All |
213466 |
1.45 % |
| Transversion |
G>C |
All |
203774 |
1.39 % |
| |
|
|
|
|
| Transition |
A>G |
Passed |
341793 |
18.89 % |
| Transition |
G>A |
Passed |
297966 |
16.47 % |
| Transition |
T>C |
Passed |
340021 |
18.79 % |
| Transition |
C>T |
Passed |
299276 |
16.54 % |
| Transversion |
A>C |
Passed |
69884 |
3.86 % |
| Transversion |
C>A |
Passed |
64563 |
3.57 % |
| Transversion |
T>G |
Passed |
69532 |
3.84 % |
| Transversion |
G>T |
Passed |
64278 |
3.55 % |
| Transversion |
A>T |
Passed |
43958 |
2.43 % |
| Transversion |
T>A |
Passed |
43562 |
2.41 % |
| Transversion |
C>G |
Passed |
87217 |
4.82 % |
| Transversion |
G>C |
Passed |
87356 |
4.83 % |
| |
|
|
|
|
| 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 |
4.36 |
11937044 |
2740043 |
| Passed |
2.41 |
1279056 |
530350 |
| dbSNPAll |
0 |
0 |
0 |
| dbSNPPassed |
0 |
0 |
0 |