/EXTERNAL BLUEPRINT/variants/K006328_15_lane_gembs
BACK
SAMPLE K006328_15_lane_gembs
Variant counts
| Type |
Total |
Pass |
% |
| SNPs |
1080895969 |
570354992 |
52.77 % |
| Multiallelic |
0 |
0 |
0.00 % |
VCF Filtering Stats
| Type |
#Sites |
% |
#Non-Variant Sites |
% |
#Variant Sites |
% |
| All |
1080895969 |
100% |
1061887959 |
98.24 % |
19008010 |
1.76 % |
| |
|
|
|
|
|
|
| Passed |
571981282 |
52.92 % |
569205786 |
53.60 % |
2775496 |
0.49 % |
| Filtered |
508914687 |
47.08 % |
492682173 |
46.40 % |
16232514 |
2.84 % |
| |
|
|
|
|
|
|
| q20 |
412089787 |
80.97 % |
410285659 |
83.28 % |
1804128 |
11.11 % |
| q20,qd2 |
62659820 |
12.31 % |
48830253 |
9.91 % |
13829567 |
85.20 % |
| q20,mq40 |
15013288 |
2.95 % |
14909447 |
3.03 % |
103841 |
0.64 % |
| qd2 |
8121043 |
1.60 % |
8012658 |
1.63 % |
108385 |
0.67 % |
| mq40 |
7447362 |
1.46 % |
7289422 |
1.48 % |
157940 |
0.97 % |
| q20,qd2,mq40 |
3465699 |
0.68 % |
3265203 |
0.66 % |
200496 |
1.24 % |
| qd2,mq40 |
102593 |
0.02 % |
89531 |
0.02 % |
13062 |
0.08 % |
| q20,qd2,fs60 |
5842 |
0.00 % |
0 |
0.00 % |
5842 |
0.04 % |
| qd2,fs60 |
3073 |
0.00 % |
0 |
0.00 % |
3073 |
0.02 % |
| fs60 |
2857 |
0.00 % |
0 |
0.00 % |
2857 |
0.02 % |
| qd2,fs60,mq40 |
1840 |
0.00 % |
0 |
0.00 % |
1840 |
0.01 % |
| q20,qd2,fs60,mq40 |
838 |
0.00 % |
0 |
0.00 % |
838 |
0.01 % |
| fs60,mq40 |
640 |
0.00 % |
0 |
0.00 % |
640 |
0.00 % |
| q20,fs60 |
4 |
0.00 % |
0 |
0.00 % |
4 |
0.00 % |
| q20,fs60,mq40 |
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 |
3126469 |
9.99 % |
| Transition |
G>A |
All |
11392443 |
36.41 % |
| Transition |
T>C |
All |
2840947 |
9.08 % |
| Transition |
C>T |
All |
11222405 |
35.86 % |
| Transversion |
A>C |
All |
204397 |
0.65 % |
| Transversion |
C>A |
All |
531274 |
1.70 % |
| Transversion |
T>G |
All |
227272 |
0.73 % |
| Transversion |
G>T |
All |
517759 |
1.65 % |
| Transversion |
A>T |
All |
422777 |
1.35 % |
| Transversion |
T>A |
All |
434139 |
1.39 % |
| Transversion |
C>G |
All |
191543 |
0.61 % |
| Transversion |
G>C |
All |
180396 |
0.58 % |
| |
|
|
|
|
| Transition |
A>G |
Passed |
336163 |
19.64 % |
| Transition |
G>A |
Passed |
291211 |
17.02 % |
| Transition |
T>C |
Passed |
334968 |
19.57 % |
| Transition |
C>T |
Passed |
290473 |
16.97 % |
| Transversion |
A>C |
Passed |
61575 |
3.60 % |
| Transversion |
C>A |
Passed |
54460 |
3.18 % |
| Transversion |
T>G |
Passed |
61394 |
3.59 % |
| Transversion |
G>T |
Passed |
54214 |
3.17 % |
| Transversion |
A>T |
Passed |
35740 |
2.09 % |
| Transversion |
T>A |
Passed |
35452 |
2.07 % |
| Transversion |
C>G |
Passed |
77831 |
4.55 % |
| Transversion |
G>C |
Passed |
77874 |
4.55 % |
| |
|
|
|
|
| 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 |
10.55 |
28582264 |
2709557 |
| Passed |
2.73 |
1252815 |
458540 |
| dbSNPAll |
0 |
0 |
0 |
| dbSNPPassed |
0 |
0 |
0 |