/EXTERNAL Roadmap/variants/K012803_1_lane_gembs
BACK
SAMPLE K012803_1_lane_gembs
Variant counts
| Type |
Total |
Pass |
% |
| SNPs |
1156173069 |
1010938041 |
87.44 % |
| Multiallelic |
0 |
0 |
0.00 % |
VCF Filtering Stats
| Type |
#Sites |
% |
#Non-Variant Sites |
% |
#Variant Sites |
% |
| All |
1156173069 |
100% |
1139488931 |
98.56 % |
16684138 |
1.44 % |
| |
|
|
|
|
|
|
| Passed |
1012221769 |
87.55 % |
1008302495 |
88.49 % |
3919274 |
0.39 % |
| Filtered |
143951300 |
12.45 % |
131186436 |
11.51 % |
12764864 |
1.26 % |
| |
|
|
|
|
|
|
| q20 |
104190155 |
72.38 % |
103117851 |
78.60 % |
1072304 |
8.40 % |
| q20,qd2 |
15831551 |
11.00 % |
4937082 |
3.76 % |
10894469 |
85.35 % |
| q20,mq40 |
14547435 |
10.11 % |
14408160 |
10.98 % |
139275 |
1.09 % |
| mq40 |
3989259 |
2.77 % |
3733764 |
2.85 % |
255495 |
2.00 % |
| q20,qd2,mq40 |
3374244 |
2.34 % |
3182489 |
2.43 % |
191755 |
1.50 % |
| qd2 |
1974631 |
1.37 % |
1772408 |
1.35 % |
202223 |
1.58 % |
| qd2,mq40 |
43114 |
0.03 % |
34682 |
0.03 % |
8432 |
0.07 % |
| qd2,fs60,mq40 |
478 |
0.00 % |
0 |
0.00 % |
478 |
0.00 % |
| fs60,mq40 |
203 |
0.00 % |
0 |
0.00 % |
203 |
0.00 % |
| qd2,fs60 |
140 |
0.00 % |
0 |
0.00 % |
140 |
0.00 % |
| fs60 |
40 |
0.00 % |
0 |
0.00 % |
40 |
0.00 % |
| q20,qd2,fs60,mq40 |
39 |
0.00 % |
0 |
0.00 % |
39 |
0.00 % |
| q20,qd2,fs60 |
10 |
0.00 % |
0 |
0.00 % |
10 |
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 |
6836902 |
37.37 % |
| Transition |
G>A |
All |
1247007 |
6.82 % |
| Transition |
T>C |
All |
6115493 |
33.43 % |
| Transition |
C>T |
All |
1319018 |
7.21 % |
| Transversion |
A>C |
All |
219374 |
1.20 % |
| Transversion |
C>A |
All |
510886 |
2.79 % |
| Transversion |
T>G |
All |
236430 |
1.29 % |
| Transversion |
G>T |
All |
496044 |
2.71 % |
| Transversion |
A>T |
All |
428934 |
2.34 % |
| Transversion |
T>A |
All |
433320 |
2.37 % |
| Transversion |
C>G |
All |
232401 |
1.27 % |
| Transversion |
G>C |
All |
218898 |
1.20 % |
| |
|
|
|
|
| Transition |
A>G |
Passed |
697398 |
18.95 % |
| Transition |
G>A |
Passed |
578725 |
15.73 % |
| Transition |
T>C |
Passed |
650358 |
17.67 % |
| Transition |
C>T |
Passed |
584502 |
15.88 % |
| Transversion |
A>C |
Passed |
146029 |
3.97 % |
| Transversion |
C>A |
Passed |
154008 |
4.18 % |
| Transversion |
T>G |
Passed |
147002 |
3.99 % |
| Transversion |
G>T |
Passed |
154374 |
4.19 % |
| Transversion |
A>T |
Passed |
135689 |
3.69 % |
| Transversion |
T>A |
Passed |
135851 |
3.69 % |
| Transversion |
C>G |
Passed |
148708 |
4.04 % |
| Transversion |
G>C |
Passed |
147511 |
4.01 % |
| |
|
|
|
|
| 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 |
5.59 |
15518420 |
2776287 |
| Passed |
2.15 |
2510983 |
1169172 |
| dbSNPAll |
0 |
0 |
0 |
| dbSNPPassed |
0 |
0 |
0 |