/EXTERNAL Roadmap/variants/K006499_1_lane_gembs
BACK
SAMPLE K006499_1_lane_gembs
Variant counts
| Type |
Total |
Pass |
% |
| SNPs |
1151553408 |
1066621189 |
92.62 % |
| Multiallelic |
0 |
0 |
0.00 % |
VCF Filtering Stats
| Type |
#Sites |
% |
#Non-Variant Sites |
% |
#Variant Sites |
% |
| All |
1151553408 |
100% |
1143789060 |
99.33 % |
7764348 |
0.67 % |
| |
|
|
|
|
|
|
| Passed |
1066820203 |
92.64 % |
1063797702 |
93.01 % |
3022501 |
0.28 % |
| Filtered |
84733205 |
7.36 % |
79991358 |
6.99 % |
4741847 |
0.44 % |
| |
|
|
|
|
|
|
| mq40 |
44047702 |
51.98 % |
43431647 |
54.30 % |
616055 |
12.99 % |
| q20,mq40 |
17847802 |
21.06 % |
17553851 |
21.94 % |
293951 |
6.20 % |
| q20 |
14755172 |
17.41 % |
14454377 |
18.07 % |
300795 |
6.34 % |
| q20,qd2 |
3240110 |
3.82 % |
818899 |
1.02 % |
2421211 |
51.06 % |
| q20,qd2,mq40 |
2656872 |
3.14 % |
2001531 |
2.50 % |
655341 |
13.82 % |
| qd2 |
1764619 |
2.08 % |
1449476 |
1.81 % |
315143 |
6.65 % |
| qd2,mq40 |
349370 |
0.41 % |
281577 |
0.35 % |
67793 |
1.43 % |
| fs60 |
30442 |
0.04 % |
0 |
0.00 % |
30442 |
0.64 % |
| q20,qd2,fs60 |
20251 |
0.02 % |
0 |
0.00 % |
20251 |
0.43 % |
| fs60,mq40 |
10537 |
0.01 % |
0 |
0.00 % |
10537 |
0.22 % |
| q20,fs60 |
6496 |
0.01 % |
0 |
0.00 % |
6496 |
0.14 % |
| qd2,fs60 |
2570 |
0.00 % |
0 |
0.00 % |
2570 |
0.05 % |
| q20,qd2,fs60,mq40 |
590 |
0.00 % |
0 |
0.00 % |
590 |
0.01 % |
| qd2,fs60,mq40 |
574 |
0.00 % |
0 |
0.00 % |
574 |
0.01 % |
| q20,fs60,mq40 |
98 |
0.00 % |
0 |
0.00 % |
98 |
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 |
2496927 |
26.77 % |
| Transition |
G>A |
All |
941815 |
10.10 % |
| Transition |
T>C |
All |
2530725 |
27.13 % |
| Transition |
C>T |
All |
948375 |
10.17 % |
| Transversion |
A>C |
All |
247636 |
2.66 % |
| Transversion |
C>A |
All |
380052 |
4.07 % |
| Transversion |
T>G |
All |
247264 |
2.65 % |
| Transversion |
G>T |
All |
382463 |
4.10 % |
| Transversion |
A>T |
All |
359157 |
3.85 % |
| Transversion |
T>A |
All |
342988 |
3.68 % |
| Transversion |
C>G |
All |
224284 |
2.40 % |
| Transversion |
G>C |
All |
225001 |
2.41 % |
| |
|
|
|
|
| Transition |
A>G |
Passed |
764536 |
18.94 % |
| Transition |
G>A |
Passed |
620716 |
15.38 % |
| Transition |
T>C |
Passed |
773989 |
19.18 % |
| Transition |
C>T |
Passed |
629907 |
15.61 % |
| Transversion |
A>C |
Passed |
164712 |
4.08 % |
| Transversion |
C>A |
Passed |
156525 |
3.88 % |
| Transversion |
T>G |
Passed |
165318 |
4.10 % |
| Transversion |
G>T |
Passed |
157655 |
3.91 % |
| Transversion |
A>T |
Passed |
142399 |
3.53 % |
| Transversion |
T>A |
Passed |
141852 |
3.51 % |
| Transversion |
C>G |
Passed |
158811 |
3.93 % |
| Transversion |
G>C |
Passed |
159616 |
3.95 % |
| |
|
|
|
|
| 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 |
2.87 |
6917842 |
2408845 |
| Passed |
2.24 |
2789148 |
1246888 |
| dbSNPAll |
0 |
0 |
0 |
| dbSNPPassed |
0 |
0 |
0 |