/EXTERNAL Roadmap/variants/K012821_1_lane_gembs
BACK
SAMPLE K012821_1_lane_gembs
Variant counts
| Type |
Total |
Pass |
% |
| SNPs |
1156859448 |
1075862703 |
93.00 % |
| Multiallelic |
0 |
0 |
0.00 % |
VCF Filtering Stats
| Type |
#Sites |
% |
#Non-Variant Sites |
% |
#Variant Sites |
% |
| All |
1156859448 |
100% |
1149468435 |
99.36 % |
7391013 |
0.64 % |
| |
|
|
|
|
|
|
| Passed |
1076000067 |
93.01 % |
1072971148 |
93.34 % |
3028919 |
0.28 % |
| Filtered |
80859381 |
6.99 % |
76497287 |
6.66 % |
4362094 |
0.41 % |
| |
|
|
|
|
|
|
| mq40 |
44405588 |
54.92 % |
43847234 |
57.32 % |
558354 |
12.80 % |
| q20,mq40 |
17774009 |
21.98 % |
17546982 |
22.94 % |
227027 |
5.20 % |
| q20 |
10975793 |
13.57 % |
10732245 |
14.03 % |
243548 |
5.58 % |
| q20,qd2 |
2883222 |
3.57 % |
785309 |
1.03 % |
2097913 |
48.09 % |
| q20,qd2,mq40 |
2404669 |
2.97 % |
1778829 |
2.33 % |
625840 |
14.35 % |
| qd2 |
1987000 |
2.46 % |
1571324 |
2.05 % |
415676 |
9.53 % |
| qd2,mq40 |
298243 |
0.37 % |
235364 |
0.31 % |
62879 |
1.44 % |
| q20,qd2,fs60 |
73278 |
0.09 % |
0 |
0.00 % |
73278 |
1.68 % |
| fs60 |
29884 |
0.04 % |
0 |
0.00 % |
29884 |
0.69 % |
| q20,fs60 |
15242 |
0.02 % |
0 |
0.00 % |
15242 |
0.35 % |
| fs60,mq40 |
8602 |
0.01 % |
0 |
0.00 % |
8602 |
0.20 % |
| qd2,fs60 |
2297 |
0.00 % |
0 |
0.00 % |
2297 |
0.05 % |
| q20,qd2,fs60,mq40 |
940 |
0.00 % |
0 |
0.00 % |
940 |
0.02 % |
| qd2,fs60,mq40 |
428 |
0.00 % |
0 |
0.00 % |
428 |
0.01 % |
| q20,fs60,mq40 |
186 |
0.00 % |
0 |
0.00 % |
186 |
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 |
2091513 |
24.06 % |
| Transition |
G>A |
All |
937687 |
10.79 % |
| Transition |
T>C |
All |
2084998 |
23.99 % |
| Transition |
C>T |
All |
956240 |
11.00 % |
| Transversion |
A>C |
All |
230001 |
2.65 % |
| Transversion |
C>A |
All |
414213 |
4.77 % |
| Transversion |
T>G |
All |
229948 |
2.65 % |
| Transversion |
G>T |
All |
435164 |
5.01 % |
| Transversion |
A>T |
All |
450967 |
5.19 % |
| Transversion |
T>A |
All |
415056 |
4.77 % |
| Transversion |
C>G |
All |
221544 |
2.55 % |
| Transversion |
G>C |
All |
225066 |
2.59 % |
| |
|
|
|
|
| Transition |
A>G |
Passed |
702708 |
18.59 % |
| Transition |
G>A |
Passed |
578666 |
15.31 % |
| Transition |
T>C |
Passed |
714115 |
18.89 % |
| Transition |
C>T |
Passed |
587894 |
15.55 % |
| Transversion |
A>C |
Passed |
154654 |
4.09 % |
| Transversion |
C>A |
Passed |
152004 |
4.02 % |
| Transversion |
T>G |
Passed |
154334 |
4.08 % |
| Transversion |
G>T |
Passed |
153137 |
4.05 % |
| Transversion |
A>T |
Passed |
139698 |
3.69 % |
| Transversion |
T>A |
Passed |
138009 |
3.65 % |
| Transversion |
C>G |
Passed |
151834 |
4.02 % |
| Transversion |
G>C |
Passed |
153711 |
4.07 % |
| |
|
|
|
|
| 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 |
2.32 |
6070438 |
2621959 |
| Passed |
2.16 |
2583383 |
1197381 |
| dbSNPAll |
0 |
0 |
0 |
| dbSNPPassed |
0 |
0 |
0 |