/EXTERNAL DEEP/variants/K009025_K009026_K009027_3_lane_gembs
BACK
SAMPLE K009025_K009026_K009027_3_lane_gembs
Variant counts
| Type |
Total |
Pass |
% |
| SNPs |
1165026242 |
713210828 |
61.22 % |
| Multiallelic |
0 |
0 |
0.00 % |
VCF Filtering Stats
| Type |
#Sites |
% |
#Non-Variant Sites |
% |
#Variant Sites |
% |
| All |
1165026242 |
100% |
1132528898 |
97.21 % |
32497344 |
2.79 % |
| |
|
|
|
|
|
|
| Passed |
718565612 |
61.68 % |
709126894 |
62.61 % |
9438718 |
1.31 % |
| Filtered |
446460630 |
38.32 % |
423402004 |
37.39 % |
23058626 |
3.21 % |
| |
|
|
|
|
|
|
| q20 |
405587001 |
90.84 % |
398817308 |
94.19 % |
6769693 |
29.36 % |
| q20,qd2 |
25534477 |
5.72 % |
9978162 |
2.36 % |
15556315 |
67.46 % |
| q20,mq40 |
8495150 |
1.90 % |
8377520 |
1.98 % |
117630 |
0.51 % |
| qd2 |
3209869 |
0.72 % |
2885534 |
0.68 % |
324335 |
1.41 % |
| q20,qd2,mq40 |
2774750 |
0.62 % |
2667154 |
0.63 % |
107596 |
0.47 % |
| mq40 |
836409 |
0.19 % |
659180 |
0.16 % |
177229 |
0.77 % |
| qd2,mq40 |
22136 |
0.00 % |
17146 |
0.00 % |
4990 |
0.02 % |
| qd2,fs60,mq40 |
359 |
0.00 % |
0 |
0.00 % |
359 |
0.00 % |
| qd2,fs60 |
170 |
0.00 % |
0 |
0.00 % |
170 |
0.00 % |
| fs60 |
118 |
0.00 % |
0 |
0.00 % |
118 |
0.00 % |
| fs60,mq40 |
106 |
0.00 % |
0 |
0.00 % |
106 |
0.00 % |
| q20,qd2,fs60,mq40 |
46 |
0.00 % |
0 |
0.00 % |
46 |
0.00 % |
| q20,qd2,fs60 |
39 |
0.00 % |
0 |
0.00 % |
39 |
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 |
10796953 |
31.41 % |
| Transition |
G>A |
All |
2412531 |
7.02 % |
| Transition |
T>C |
All |
12113405 |
35.24 % |
| Transition |
C>T |
All |
1732436 |
5.04 % |
| Transversion |
A>C |
All |
451318 |
1.31 % |
| Transversion |
C>A |
All |
1644149 |
4.78 % |
| Transversion |
T>G |
All |
554229 |
1.61 % |
| Transversion |
G>T |
All |
1544157 |
4.49 % |
| Transversion |
A>T |
All |
952154 |
2.77 % |
| Transversion |
T>A |
All |
1074551 |
3.13 % |
| Transversion |
C>G |
All |
560540 |
1.63 % |
| Transversion |
G>C |
All |
537040 |
1.56 % |
| |
|
|
|
|
| Transition |
A>G |
Passed |
1008396 |
20.62 % |
| Transition |
G>A |
Passed |
593181 |
12.13 % |
| Transition |
T>C |
Passed |
1471229 |
30.09 % |
| Transition |
C>T |
Passed |
503889 |
10.30 % |
| Transversion |
A>C |
Passed |
148030 |
3.03 % |
| Transversion |
C>A |
Passed |
206559 |
4.22 % |
| Transversion |
T>G |
Passed |
165775 |
3.39 % |
| Transversion |
G>T |
Passed |
179062 |
3.66 % |
| Transversion |
A>T |
Passed |
132917 |
2.72 % |
| Transversion |
T>A |
Passed |
164325 |
3.36 % |
| Transversion |
C>G |
Passed |
158632 |
3.24 % |
| Transversion |
G>C |
Passed |
157876 |
3.23 % |
| |
|
|
|
|
| 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 |
3.70 |
27055325 |
7318138 |
| Passed |
2.72 |
3576695 |
1313176 |
| dbSNPAll |
0 |
0 |
0 |
| dbSNPPassed |
0 |
0 |
0 |