/EXTERNAL BLUEPRINT/variants/K011720_1_lane_gembs
BACK
SAMPLE K011720_1_lane_gembs
Variant counts
| Type |
Total |
Pass |
% |
| SNPs |
605596610 |
176449 |
0.03 % |
| Multiallelic |
0 |
0 |
0.00 % |
VCF Filtering Stats
| Type |
#Sites |
% |
#Non-Variant Sites |
% |
#Variant Sites |
% |
| All |
605596610 |
100% |
600137922 |
99.10 % |
5458688 |
0.90 % |
| |
|
|
|
|
|
|
| Passed |
2930157 |
0.48 % |
124198 |
0.02 % |
2805959 |
95.76 % |
| Filtered |
602666453 |
99.52 % |
600013724 |
99.98 % |
2652729 |
90.53 % |
| |
|
|
|
|
|
|
| q20 |
378887122 |
62.87 % |
376779080 |
62.80 % |
2108042 |
79.47 % |
| q20,qd2 |
169043712 |
28.05 % |
168814112 |
28.14 % |
229600 |
8.66 % |
| q20,mq40 |
33768110 |
5.60 % |
33632684 |
5.61 % |
135426 |
5.11 % |
| q20,qd2,mq40 |
20787144 |
3.45 % |
20768093 |
3.46 % |
19051 |
0.72 % |
| mq40 |
176681 |
0.03 % |
16184 |
0.00 % |
160497 |
6.05 % |
| qd2 |
3277 |
0.00 % |
3245 |
0.00 % |
32 |
0.00 % |
| qd2,mq40 |
380 |
0.00 % |
326 |
0.00 % |
54 |
0.00 % |
| qd2,fs60 |
13 |
0.00 % |
0 |
0.00 % |
13 |
0.00 % |
| fs60,mq40 |
5 |
0.00 % |
0 |
0.00 % |
5 |
0.00 % |
| fs60 |
3 |
0.00 % |
0 |
0.00 % |
3 |
0.00 % |
| q20,qd2,fs60,mq40 |
3 |
0.00 % |
0 |
0.00 % |
3 |
0.00 % |
| qd2,fs60,mq40 |
2 |
0.00 % |
0 |
0.00 % |
2 |
0.00 % |
| q20,qd2,fs60 |
1 |
0.00 % |
0 |
0.00 % |
1 |
0.00 % |
| q20,fs60 |
0 |
0.00 % |
0 |
0.00 % |
0 |
0.00 % |
| q20,fs60,mq40 |
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 |
2211416 |
22.71 % |
| Transition |
G>A |
All |
781787 |
8.03 % |
| Transition |
T>C |
All |
2900739 |
29.80 % |
| Transition |
C>T |
All |
386741 |
3.97 % |
| Transversion |
A>C |
All |
361029 |
3.71 % |
| Transversion |
C>A |
All |
529582 |
5.44 % |
| Transversion |
T>G |
All |
449706 |
4.62 % |
| Transversion |
G>T |
All |
480751 |
4.94 % |
| Transversion |
A>T |
All |
403206 |
4.14 % |
| Transversion |
T>A |
All |
554055 |
5.69 % |
| Transversion |
C>G |
All |
310313 |
3.19 % |
| Transversion |
G>C |
All |
366214 |
3.76 % |
| |
|
|
|
|
| Transition |
A>G |
Passed |
7614 |
14.88 % |
| Transition |
G>A |
Passed |
7676 |
15.00 % |
| Transition |
T>C |
Passed |
13150 |
25.70 % |
| Transition |
C>T |
Passed |
3094 |
6.05 % |
| Transversion |
A>C |
Passed |
2363 |
4.62 % |
| Transversion |
C>A |
Passed |
3192 |
6.24 % |
| Transversion |
T>G |
Passed |
2426 |
4.74 % |
| Transversion |
G>T |
Passed |
1686 |
3.30 % |
| Transversion |
A>T |
Passed |
1059 |
2.07 % |
| Transversion |
T>A |
Passed |
2743 |
5.36 % |
| Transversion |
C>G |
Passed |
2405 |
4.70 % |
| Transversion |
G>C |
Passed |
3750 |
7.33 % |
| |
|
|
|
|
| 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 |
1.82 |
6280683 |
3454856 |
| Passed |
1.61 |
31534 |
19624 |
| dbSNPAll |
0 |
0 |
0 |
| dbSNPPassed |
0 |
0 |
0 |