/EXTERNAL Roadmap/variants/K006506_1_lane_gembs
BACK
SAMPLE K006506_1_lane_gembs
Variant counts
| Type |
Total |
Pass |
% |
| SNPs |
1157338683 |
1062440978 |
91.80 % |
| Multiallelic |
0 |
0 |
0.00 % |
VCF Filtering Stats
| Type |
#Sites |
% |
#Non-Variant Sites |
% |
#Variant Sites |
% |
| All |
1157338683 |
100% |
1148770413 |
99.26 % |
8568270 |
0.74 % |
| |
|
|
|
|
|
|
| Passed |
1062719418 |
91.82 % |
1059596608 |
92.24 % |
3122810 |
0.29 % |
| Filtered |
94619265 |
8.18 % |
89173805 |
7.76 % |
5445460 |
0.51 % |
| |
|
|
|
|
|
|
| mq40 |
43773089 |
46.26 % |
43148440 |
48.39 % |
624649 |
11.47 % |
| q20 |
23113857 |
24.43 % |
22716127 |
25.47 % |
397730 |
7.30 % |
| q20,mq40 |
18806782 |
19.88 % |
18534907 |
20.79 % |
271875 |
4.99 % |
| q20,qd2 |
3966901 |
4.19 % |
960166 |
1.08 % |
3006735 |
55.22 % |
| q20,qd2,mq40 |
2647488 |
2.80 % |
1953994 |
2.19 % |
693494 |
12.74 % |
| qd2 |
1895793 |
2.00 % |
1570370 |
1.76 % |
325423 |
5.98 % |
| qd2,mq40 |
355537 |
0.38 % |
289801 |
0.32 % |
65736 |
1.21 % |
| fs60 |
30165 |
0.03 % |
0 |
0.00 % |
30165 |
0.55 % |
| q20,qd2,fs60 |
10917 |
0.01 % |
0 |
0.00 % |
10917 |
0.20 % |
| fs60,mq40 |
10741 |
0.01 % |
0 |
0.00 % |
10741 |
0.20 % |
| q20,fs60 |
4007 |
0.00 % |
0 |
0.00 % |
4007 |
0.07 % |
| qd2,fs60 |
2644 |
0.00 % |
0 |
0.00 % |
2644 |
0.05 % |
| qd2,fs60,mq40 |
643 |
0.00 % |
0 |
0.00 % |
643 |
0.01 % |
| q20,qd2,fs60,mq40 |
586 |
0.00 % |
0 |
0.00 % |
586 |
0.01 % |
| q20,fs60,mq40 |
115 |
0.00 % |
0 |
0.00 % |
115 |
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 |
2869309 |
28.40 % |
| Transition |
G>A |
All |
999782 |
9.90 % |
| Transition |
T>C |
All |
2878659 |
28.49 % |
| Transition |
C>T |
All |
1005489 |
9.95 % |
| Transversion |
A>C |
All |
240180 |
2.38 % |
| Transversion |
C>A |
All |
375951 |
3.72 % |
| Transversion |
T>G |
All |
243502 |
2.41 % |
| Transversion |
G>T |
All |
379053 |
3.75 % |
| Transversion |
A>T |
All |
336379 |
3.33 % |
| Transversion |
T>A |
All |
327091 |
3.24 % |
| Transversion |
C>G |
All |
224046 |
2.22 % |
| Transversion |
G>C |
All |
224375 |
2.22 % |
| |
|
|
|
|
| Transition |
A>G |
Passed |
774529 |
19.07 % |
| Transition |
G>A |
Passed |
620575 |
15.28 % |
| Transition |
T>C |
Passed |
798193 |
19.65 % |
| Transition |
C>T |
Passed |
629433 |
15.49 % |
| Transversion |
A>C |
Passed |
163757 |
4.03 % |
| Transversion |
C>A |
Passed |
155657 |
3.83 % |
| Transversion |
T>G |
Passed |
163920 |
4.03 % |
| Transversion |
G>T |
Passed |
156593 |
3.85 % |
| Transversion |
A>T |
Passed |
141645 |
3.49 % |
| Transversion |
T>A |
Passed |
140834 |
3.47 % |
| Transversion |
C>G |
Passed |
158031 |
3.89 % |
| Transversion |
G>C |
Passed |
159316 |
3.92 % |
| |
|
|
|
|
| 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 |
3.30 |
7753239 |
2350577 |
| Passed |
2.28 |
2822730 |
1239753 |
| dbSNPAll |
0 |
0 |
0 |
| dbSNPPassed |
0 |
0 |
0 |