/EXTERNAL Roadmap/variants/K012815_1_lane_gembs
BACK
SAMPLE K012815_1_lane_gembs
Variant counts
| Type |
Total |
Pass |
% |
| SNPs |
1172641652 |
724506007 |
61.78 % |
| Multiallelic |
0 |
0 |
0.00 % |
VCF Filtering Stats
| Type |
#Sites |
% |
#Non-Variant Sites |
% |
#Variant Sites |
% |
| All |
1172641652 |
100% |
1135464775 |
96.83 % |
37176877 |
3.17 % |
| |
|
|
|
|
|
|
| Passed |
730370597 |
62.28 % |
721602217 |
63.55 % |
8768380 |
1.20 % |
| Filtered |
442271055 |
37.72 % |
413862558 |
36.45 % |
28408497 |
3.89 % |
| |
|
|
|
|
|
|
| q20 |
384096200 |
86.85 % |
379069414 |
91.59 % |
5026786 |
17.69 % |
| q20,qd2 |
33953140 |
7.68 % |
11311047 |
2.73 % |
22642093 |
79.70 % |
| q20,mq40 |
17211914 |
3.89 % |
17054025 |
4.12 % |
157889 |
0.56 % |
| q20,qd2,mq40 |
3885288 |
0.88 % |
3722525 |
0.90 % |
162763 |
0.57 % |
| mq40 |
1715887 |
0.39 % |
1432002 |
0.35 % |
283885 |
1.00 % |
| qd2 |
1372886 |
0.31 % |
1246104 |
0.30 % |
126782 |
0.45 % |
| qd2,mq40 |
34890 |
0.01 % |
27441 |
0.01 % |
7449 |
0.03 % |
| qd2,fs60,mq40 |
448 |
0.00 % |
0 |
0.00 % |
448 |
0.00 % |
| fs60,mq40 |
209 |
0.00 % |
0 |
0.00 % |
209 |
0.00 % |
| qd2,fs60 |
126 |
0.00 % |
0 |
0.00 % |
126 |
0.00 % |
| q20,qd2,fs60,mq40 |
35 |
0.00 % |
0 |
0.00 % |
35 |
0.00 % |
| fs60 |
22 |
0.00 % |
0 |
0.00 % |
22 |
0.00 % |
| q20,qd2,fs60 |
8 |
0.00 % |
0 |
0.00 % |
8 |
0.00 % |
| q20,fs60,mq40 |
2 |
0.00 % |
0 |
0.00 % |
2 |
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 |
15933798 |
40.95 % |
| Transition |
G>A |
All |
2351980 |
6.04 % |
| Transition |
T>C |
All |
10709386 |
27.52 % |
| Transition |
C>T |
All |
2520576 |
6.48 % |
| Transversion |
A>C |
All |
421993 |
1.08 % |
| Transversion |
C>A |
All |
1423730 |
3.66 % |
| Transversion |
T>G |
All |
664748 |
1.71 % |
| Transversion |
G>T |
All |
1292230 |
3.32 % |
| Transversion |
A>T |
All |
1201649 |
3.09 % |
| Transversion |
T>A |
All |
1357251 |
3.49 % |
| Transversion |
C>G |
All |
614009 |
1.58 % |
| Transversion |
G>C |
All |
419206 |
1.08 % |
| |
|
|
|
|
| Transition |
A>G |
Passed |
962783 |
26.09 % |
| Transition |
G>A |
Passed |
480238 |
13.02 % |
| Transition |
T>C |
Passed |
606594 |
16.44 % |
| Transition |
C>T |
Passed |
496300 |
13.45 % |
| Transversion |
A>C |
Passed |
140004 |
3.79 % |
| Transversion |
C>A |
Passed |
146271 |
3.96 % |
| Transversion |
T>G |
Passed |
152619 |
4.14 % |
| Transversion |
G>T |
Passed |
147801 |
4.01 % |
| Transversion |
A>T |
Passed |
135968 |
3.69 % |
| Transversion |
T>A |
Passed |
136545 |
3.70 % |
| Transversion |
C>G |
Passed |
146404 |
3.97 % |
| Transversion |
G>C |
Passed |
138072 |
3.74 % |
| |
|
|
|
|
| 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 |
4.26 |
31515740 |
7394816 |
| Passed |
2.23 |
2545915 |
1143684 |
| dbSNPAll |
0 |
0 |
0 |
| dbSNPPassed |
0 |
0 |
0 |