/EXTERNAL BLUEPRINT/variants/K006329_15_lane_gembs
BACK
SAMPLE K006329_15_lane_gembs
Variant counts
| Type |
Total |
Pass |
% |
| SNPs |
1052841296 |
508513475 |
48.30 % |
| Multiallelic |
0 |
0 |
0.00 % |
VCF Filtering Stats
| Type |
#Sites |
% |
#Non-Variant Sites |
% |
#Variant Sites |
% |
| All |
1052841296 |
100% |
1034514207 |
98.26 % |
18327089 |
1.74 % |
| |
|
|
|
|
|
|
| Passed |
510117790 |
48.45 % |
507459580 |
49.05 % |
2658210 |
0.52 % |
| Filtered |
542723506 |
51.55 % |
527054627 |
50.95 % |
15668879 |
3.07 % |
| |
|
|
|
|
|
|
| q20 |
441118777 |
81.28 % |
439339916 |
83.36 % |
1778861 |
11.35 % |
| q20,qd2 |
68676031 |
12.65 % |
55350849 |
10.50 % |
13325182 |
85.04 % |
| q20,mq40 |
16429327 |
3.03 % |
16325745 |
3.10 % |
103582 |
0.66 % |
| mq40 |
6603783 |
1.22 % |
6452026 |
1.22 % |
151757 |
0.97 % |
| qd2 |
6028658 |
1.11 % |
5935808 |
1.13 % |
92850 |
0.59 % |
| q20,qd2,mq40 |
3772554 |
0.70 % |
3579462 |
0.68 % |
193092 |
1.23 % |
| qd2,mq40 |
81645 |
0.02 % |
70821 |
0.01 % |
10824 |
0.07 % |
| q20,qd2,fs60 |
4674 |
0.00 % |
0 |
0.00 % |
4674 |
0.03 % |
| qd2,fs60 |
2794 |
0.00 % |
0 |
0.00 % |
2794 |
0.02 % |
| fs60 |
2471 |
0.00 % |
0 |
0.00 % |
2471 |
0.02 % |
| qd2,fs60,mq40 |
1546 |
0.00 % |
0 |
0.00 % |
1546 |
0.01 % |
| q20,qd2,fs60,mq40 |
736 |
0.00 % |
0 |
0.00 % |
736 |
0.00 % |
| fs60,mq40 |
506 |
0.00 % |
0 |
0.00 % |
506 |
0.00 % |
| q20,fs60 |
3 |
0.00 % |
0 |
0.00 % |
3 |
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 |
2998079 |
10.35 % |
| Transition |
G>A |
All |
10366181 |
35.80 % |
| Transition |
T>C |
All |
2679547 |
9.25 % |
| Transition |
C>T |
All |
10173117 |
35.13 % |
| Transversion |
A>C |
All |
202652 |
0.70 % |
| Transversion |
C>A |
All |
544906 |
1.88 % |
| Transversion |
T>G |
All |
230670 |
0.80 % |
| Transversion |
G>T |
All |
526434 |
1.82 % |
| Transversion |
A>T |
All |
423552 |
1.46 % |
| Transversion |
T>A |
All |
438047 |
1.51 % |
| Transversion |
C>G |
All |
194275 |
0.67 % |
| Transversion |
G>C |
All |
181131 |
0.63 % |
| |
|
|
|
|
| Transition |
A>G |
Passed |
310637 |
20.00 % |
| Transition |
G>A |
Passed |
266125 |
17.13 % |
| Transition |
T>C |
Passed |
308647 |
19.87 % |
| Transition |
C>T |
Passed |
265176 |
17.07 % |
| Transversion |
A>C |
Passed |
53594 |
3.45 % |
| Transversion |
C>A |
Passed |
46971 |
3.02 % |
| Transversion |
T>G |
Passed |
53816 |
3.46 % |
| Transversion |
G>T |
Passed |
47527 |
3.06 % |
| Transversion |
A>T |
Passed |
29732 |
1.91 % |
| Transversion |
T>A |
Passed |
29619 |
1.91 % |
| Transversion |
C>G |
Passed |
70511 |
4.54 % |
| Transversion |
G>C |
Passed |
70827 |
4.56 % |
| |
|
|
|
|
| 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 |
26216924 |
2741667 |
| Passed |
2.86 |
1150585 |
402597 |
| dbSNPAll |
0 |
0 |
0 |
| dbSNPPassed |
0 |
0 |
0 |