/EXTERNAL Roadmap/variants/K012817_1_lane_gembs
BACK
SAMPLE K012817_1_lane_gembs
Variant counts
| Type |
Total |
Pass |
% |
| SNPs |
1164673215 |
760835477 |
65.33 % |
| Multiallelic |
0 |
0 |
0.00 % |
VCF Filtering Stats
| Type |
#Sites |
% |
#Non-Variant Sites |
% |
#Variant Sites |
% |
| All |
1164673215 |
100% |
1138763175 |
97.78 % |
25910040 |
2.22 % |
| |
|
|
|
|
|
|
| Passed |
765050062 |
65.69 % |
758324951 |
66.59 % |
6725111 |
0.88 % |
| Filtered |
399623153 |
34.31 % |
380438224 |
33.41 % |
19184929 |
2.51 % |
| |
|
|
|
|
|
|
| q20 |
353021371 |
88.34 % |
349745652 |
91.93 % |
3275719 |
17.07 % |
| q20,qd2 |
24228958 |
6.06 % |
8987306 |
2.36 % |
15241652 |
79.45 % |
| q20,mq40 |
14639741 |
3.66 % |
14512497 |
3.81 % |
127244 |
0.66 % |
| q20,qd2,mq40 |
3504547 |
0.88 % |
3351691 |
0.88 % |
152856 |
0.80 % |
| qd2 |
2178174 |
0.55 % |
2034000 |
0.53 % |
144174 |
0.75 % |
| mq40 |
2009433 |
0.50 % |
1774960 |
0.47 % |
234473 |
1.22 % |
| qd2,mq40 |
39797 |
0.01 % |
32118 |
0.01 % |
7679 |
0.04 % |
| qd2,fs60,mq40 |
604 |
0.00 % |
0 |
0.00 % |
604 |
0.00 % |
| fs60,mq40 |
255 |
0.00 % |
0 |
0.00 % |
255 |
0.00 % |
| qd2,fs60 |
158 |
0.00 % |
0 |
0.00 % |
158 |
0.00 % |
| fs60 |
51 |
0.00 % |
0 |
0.00 % |
51 |
0.00 % |
| q20,qd2,fs60,mq40 |
47 |
0.00 % |
0 |
0.00 % |
47 |
0.00 % |
| q20,qd2,fs60 |
16 |
0.00 % |
0 |
0.00 % |
16 |
0.00 % |
| q20,fs60,mq40 |
1 |
0.00 % |
0 |
0.00 % |
1 |
0.00 % |
| q20,fs60 |
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 |
10665774 |
38.57 % |
| Transition |
G>A |
All |
1800246 |
6.51 % |
| Transition |
T>C |
All |
8192075 |
29.63 % |
| Transition |
C>T |
All |
1895850 |
6.86 % |
| Transversion |
A>C |
All |
307606 |
1.11 % |
| Transversion |
C>A |
All |
1031769 |
3.73 % |
| Transversion |
T>G |
All |
428107 |
1.55 % |
| Transversion |
G>T |
All |
954533 |
3.45 % |
| Transversion |
A>T |
All |
778774 |
2.82 % |
| Transversion |
T>A |
All |
851049 |
3.08 % |
| Transversion |
C>G |
All |
425449 |
1.54 % |
| Transversion |
G>C |
All |
320832 |
1.16 % |
| |
|
|
|
|
| Transition |
A>G |
Passed |
705537 |
20.93 % |
| Transition |
G>A |
Passed |
492585 |
14.61 % |
| Transition |
T>C |
Passed |
583625 |
17.32 % |
| Transition |
C>T |
Passed |
501440 |
14.88 % |
| Transversion |
A>C |
Passed |
134671 |
4.00 % |
| Transversion |
C>A |
Passed |
142936 |
4.24 % |
| Transversion |
T>G |
Passed |
138275 |
4.10 % |
| Transversion |
G>T |
Passed |
143487 |
4.26 % |
| Transversion |
A>T |
Passed |
128036 |
3.80 % |
| Transversion |
T>A |
Passed |
128836 |
3.82 % |
| Transversion |
C>G |
Passed |
136829 |
4.06 % |
| Transversion |
G>C |
Passed |
134181 |
3.98 % |
| |
|
|
|
|
| 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 |
4.42 |
22553945 |
5098119 |
| Passed |
2.10 |
2283187 |
1087251 |
| dbSNPAll |
0 |
0 |
0 |
| dbSNPPassed |
0 |
0 |
0 |