/EXTERNAL Roadmap/variants/K006486_1_lane_gembs
BACK
SAMPLE K006486_1_lane_gembs
Variant counts
| Type |
Total |
Pass |
% |
| SNPs |
1156580020 |
1065311505 |
92.11 % |
| Multiallelic |
0 |
0 |
0.00 % |
VCF Filtering Stats
| Type |
#Sites |
% |
#Non-Variant Sites |
% |
#Variant Sites |
% |
| All |
1156580020 |
100% |
1148805340 |
99.33 % |
7774680 |
0.67 % |
| |
|
|
|
|
|
|
| Passed |
1065533277 |
92.13 % |
1062510670 |
92.49 % |
3022607 |
0.28 % |
| Filtered |
91046743 |
7.87 % |
86294670 |
7.51 % |
4752073 |
0.45 % |
| |
|
|
|
|
|
|
| mq40 |
44772082 |
49.17 % |
44168921 |
51.18 % |
603161 |
12.69 % |
| q20 |
19539802 |
21.46 % |
19196815 |
22.25 % |
342987 |
7.22 % |
| q20,mq40 |
18762989 |
20.61 % |
18501946 |
21.44 % |
261043 |
5.49 % |
| q20,qd2 |
3281189 |
3.60 % |
832635 |
0.96 % |
2448554 |
51.53 % |
| q20,qd2,mq40 |
2539455 |
2.79 % |
1881256 |
2.18 % |
658199 |
13.85 % |
| qd2 |
1745405 |
1.92 % |
1443065 |
1.67 % |
302340 |
6.36 % |
| qd2,mq40 |
334734 |
0.37 % |
270032 |
0.31 % |
64702 |
1.36 % |
| fs60 |
26012 |
0.03 % |
0 |
0.00 % |
26012 |
0.55 % |
| q20,qd2,fs60 |
24109 |
0.03 % |
0 |
0.00 % |
24109 |
0.51 % |
| fs60,mq40 |
8909 |
0.01 % |
0 |
0.00 % |
8909 |
0.19 % |
| q20,fs60 |
8370 |
0.01 % |
0 |
0.00 % |
8370 |
0.18 % |
| qd2,fs60 |
2391 |
0.00 % |
0 |
0.00 % |
2391 |
0.05 % |
| q20,qd2,fs60,mq40 |
640 |
0.00 % |
0 |
0.00 % |
640 |
0.01 % |
| qd2,fs60,mq40 |
527 |
0.00 % |
0 |
0.00 % |
527 |
0.01 % |
| q20,fs60,mq40 |
129 |
0.00 % |
0 |
0.00 % |
129 |
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 |
2488778 |
26.75 % |
| Transition |
G>A |
All |
970536 |
10.43 % |
| Transition |
T>C |
All |
2500847 |
26.88 % |
| Transition |
C>T |
All |
977876 |
10.51 % |
| Transversion |
A>C |
All |
239758 |
2.58 % |
| Transversion |
C>A |
All |
378916 |
4.07 % |
| Transversion |
T>G |
All |
242147 |
2.60 % |
| Transversion |
G>T |
All |
385542 |
4.14 % |
| Transversion |
A>T |
All |
340648 |
3.66 % |
| Transversion |
T>A |
All |
331710 |
3.56 % |
| Transversion |
C>G |
All |
223877 |
2.41 % |
| Transversion |
G>C |
All |
224713 |
2.41 % |
| |
|
|
|
|
| Transition |
A>G |
Passed |
754337 |
18.75 % |
| Transition |
G>A |
Passed |
619996 |
15.41 % |
| Transition |
T>C |
Passed |
776917 |
19.32 % |
| Transition |
C>T |
Passed |
628300 |
15.62 % |
| Transversion |
A>C |
Passed |
163880 |
4.07 % |
| Transversion |
C>A |
Passed |
156389 |
3.89 % |
| Transversion |
T>G |
Passed |
163564 |
4.07 % |
| Transversion |
G>T |
Passed |
157335 |
3.91 % |
| Transversion |
A>T |
Passed |
141979 |
3.53 % |
| Transversion |
T>A |
Passed |
141493 |
3.52 % |
| Transversion |
C>G |
Passed |
158329 |
3.94 % |
| Transversion |
G>C |
Passed |
159800 |
3.97 % |
| |
|
|
|
|
| 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 |
2.93 |
6938037 |
2367311 |
| Passed |
2.24 |
2779550 |
1242769 |
| dbSNPAll |
0 |
0 |
0 |
| dbSNPPassed |
0 |
0 |
0 |