/EXTERNAL Roadmap/variants/K012813_1_lane_gembs
BACK
SAMPLE K012813_1_lane_gembs
Variant counts
| Type |
Total |
Pass |
% |
| SNPs |
1142668718 |
60156659 |
5.26 % |
| Multiallelic |
0 |
0 |
0.00 % |
VCF Filtering Stats
| Type |
#Sites |
% |
#Non-Variant Sites |
% |
#Variant Sites |
% |
| All |
1142668718 |
100% |
1116506052 |
97.71 % |
26162666 |
2.29 % |
| |
|
|
|
|
|
|
| Passed |
69928218 |
6.12 % |
59250815 |
5.31 % |
10677403 |
15.27 % |
| Filtered |
1072740500 |
93.88 % |
1057255237 |
94.69 % |
15485263 |
22.14 % |
| |
|
|
|
|
|
|
| q20 |
1005831951 |
93.76 % |
998077507 |
94.40 % |
7754444 |
50.08 % |
| q20,qd2 |
41463542 |
3.87 % |
34093544 |
3.22 % |
7369998 |
47.59 % |
| q20,mq40 |
18503198 |
1.72 % |
18385398 |
1.74 % |
117800 |
0.76 % |
| q20,qd2,mq40 |
6606348 |
0.62 % |
6528245 |
0.62 % |
78103 |
0.50 % |
| mq40 |
301732 |
0.03 % |
142279 |
0.01 % |
159453 |
1.03 % |
| qd2 |
19429 |
0.00 % |
17169 |
0.00 % |
2260 |
0.01 % |
| qd2,mq40 |
14027 |
0.00 % |
11095 |
0.00 % |
2932 |
0.02 % |
| qd2,fs60,mq40 |
140 |
0.00 % |
0 |
0.00 % |
140 |
0.00 % |
| fs60,mq40 |
65 |
0.00 % |
0 |
0.00 % |
65 |
0.00 % |
| qd2,fs60 |
54 |
0.00 % |
0 |
0.00 % |
54 |
0.00 % |
| q20,qd2,fs60,mq40 |
8 |
0.00 % |
0 |
0.00 % |
8 |
0.00 % |
| fs60 |
5 |
0.00 % |
0 |
0.00 % |
5 |
0.00 % |
| q20,qd2,fs60 |
1 |
0.00 % |
0 |
0.00 % |
1 |
0.00 % |
| q20,fs60 |
0 |
0.00 % |
0 |
0.00 % |
0 |
0.00 % |
| q20,fs60,mq40 |
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 |
9489212 |
33.32 % |
| Transition |
G>A |
All |
1328748 |
4.67 % |
| Transition |
T>C |
All |
5018542 |
17.62 % |
| Transition |
C>T |
All |
1491538 |
5.24 % |
| Transversion |
A>C |
All |
593892 |
2.09 % |
| Transversion |
C>A |
All |
1994278 |
7.00 % |
| Transversion |
T>G |
All |
1364986 |
4.79 % |
| Transversion |
G>T |
All |
1686769 |
5.92 % |
| Transversion |
A>T |
All |
1803672 |
6.33 % |
| Transversion |
T>A |
All |
2346443 |
8.24 % |
| Transversion |
C>G |
All |
867821 |
3.05 % |
| Transversion |
G>C |
All |
492992 |
1.73 % |
| |
|
|
|
|
| Transition |
A>G |
Passed |
170746 |
17.84 % |
| Transition |
G>A |
Passed |
113348 |
11.84 % |
| Transition |
T>C |
Passed |
129478 |
13.53 % |
| Transition |
C>T |
Passed |
119692 |
12.51 % |
| Transversion |
A>C |
Passed |
51662 |
5.40 % |
| Transversion |
C>A |
Passed |
53997 |
5.64 % |
| Transversion |
T>G |
Passed |
57215 |
5.98 % |
| Transversion |
G>T |
Passed |
54755 |
5.72 % |
| Transversion |
A>T |
Passed |
48747 |
5.09 % |
| Transversion |
T>A |
Passed |
49080 |
5.13 % |
| Transversion |
C>G |
Passed |
55659 |
5.82 % |
| Transversion |
G>C |
Passed |
52570 |
5.49 % |
| |
|
|
|
|
| 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 |
1.55 |
17328040 |
11150853 |
| Passed |
1.26 |
533264 |
423685 |
| dbSNPAll |
0 |
0 |
0 |
| dbSNPPassed |
0 |
0 |
0 |