/EXTERNAL Roadmap/variants/K012810_1_lane_gembs
BACK
SAMPLE K012810_1_lane_gembs
Variant counts
| Type |
Total |
Pass |
% |
| SNPs |
1168360653 |
950961248 |
81.39 % |
| Multiallelic |
0 |
0 |
0.00 % |
VCF Filtering Stats
| Type |
#Sites |
% |
#Non-Variant Sites |
% |
#Variant Sites |
% |
| All |
1168360653 |
100% |
1142867596 |
97.82 % |
25493057 |
2.18 % |
| |
|
|
|
|
|
|
| Passed |
953383699 |
81.60 % |
947870931 |
82.94 % |
5512768 |
0.58 % |
| Filtered |
214976954 |
18.40 % |
194996665 |
17.06 % |
19980289 |
2.10 % |
| |
|
|
|
|
|
|
| q20 |
165369834 |
76.92 % |
163187928 |
83.69 % |
2181906 |
10.92 % |
| q20,qd2 |
24357369 |
11.33 % |
7445383 |
3.82 % |
16911986 |
84.64 % |
| q20,mq40 |
15915721 |
7.40 % |
15760441 |
8.08 % |
155280 |
0.78 % |
| q20,qd2,mq40 |
3585259 |
1.67 % |
3388454 |
1.74 % |
196805 |
0.98 % |
| mq40 |
3511476 |
1.63 % |
3232493 |
1.66 % |
278983 |
1.40 % |
| qd2 |
2198529 |
1.02 % |
1951508 |
1.00 % |
247021 |
1.24 % |
| qd2,mq40 |
38016 |
0.02 % |
30458 |
0.02 % |
7558 |
0.04 % |
| qd2,fs60,mq40 |
387 |
0.00 % |
0 |
0.00 % |
387 |
0.00 % |
| fs60,mq40 |
197 |
0.00 % |
0 |
0.00 % |
197 |
0.00 % |
| qd2,fs60 |
100 |
0.00 % |
0 |
0.00 % |
100 |
0.00 % |
| fs60 |
31 |
0.00 % |
0 |
0.00 % |
31 |
0.00 % |
| q20,qd2,fs60,mq40 |
24 |
0.00 % |
0 |
0.00 % |
24 |
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 |
11357462 |
42.01 % |
| Transition |
G>A |
All |
1619609 |
5.99 % |
| Transition |
T>C |
All |
8606537 |
31.83 % |
| Transition |
C>T |
All |
1834949 |
6.79 % |
| Transversion |
A>C |
All |
267391 |
0.99 % |
| Transversion |
C>A |
All |
674813 |
2.50 % |
| Transversion |
T>G |
All |
342877 |
1.27 % |
| Transversion |
G>T |
All |
619474 |
2.29 % |
| Transversion |
A>T |
All |
534336 |
1.98 % |
| Transversion |
T>A |
All |
588606 |
2.18 % |
| Transversion |
C>G |
All |
324125 |
1.20 % |
| Transversion |
G>C |
All |
266313 |
0.99 % |
| |
|
|
|
|
| Transition |
A>G |
Passed |
942345 |
23.66 % |
| Transition |
G>A |
Passed |
564492 |
14.18 % |
| Transition |
T>C |
Passed |
686166 |
17.23 % |
| Transition |
C>T |
Passed |
577933 |
14.51 % |
| Transversion |
A>C |
Passed |
150589 |
3.78 % |
| Transversion |
C>A |
Passed |
156609 |
3.93 % |
| Transversion |
T>G |
Passed |
155397 |
3.90 % |
| Transversion |
G>T |
Passed |
158190 |
3.97 % |
| Transversion |
A>T |
Passed |
140267 |
3.52 % |
| Transversion |
T>A |
Passed |
139812 |
3.51 % |
| Transversion |
C>G |
Passed |
156482 |
3.93 % |
| Transversion |
G>C |
Passed |
153982 |
3.87 % |
| |
|
|
|
|
| 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 |
6.47 |
23418557 |
3617935 |
| Passed |
2.29 |
2770936 |
1211328 |
| dbSNPAll |
0 |
0 |
0 |
| dbSNPPassed |
0 |
0 |
0 |