/EXTERNAL Roadmap/variants/K006497_K006498_2_lane_gembs
BACK
SAMPLE K006497_K006498_2_lane_gembs
Variant counts
| Type |
Total |
Pass |
% |
| SNPs |
1138714342 |
669592893 |
58.80 % |
| Multiallelic |
0 |
0 |
0.00 % |
VCF Filtering Stats
| Type |
#Sites |
% |
#Non-Variant Sites |
% |
#Variant Sites |
% |
| All |
1138714342 |
100% |
1117416697 |
98.13 % |
21297645 |
1.87 % |
| |
|
|
|
|
|
|
| Passed |
671701863 |
58.99 % |
668192108 |
59.80 % |
3509755 |
0.52 % |
| Filtered |
467012479 |
41.01 % |
449224589 |
40.20 % |
17787890 |
2.65 % |
| |
|
|
|
|
|
|
| q20 |
320075998 |
68.54 % |
312800290 |
69.63 % |
7275708 |
40.90 % |
| qd2 |
62435812 |
13.37 % |
62225552 |
13.85 % |
210260 |
1.18 % |
| q20,qd2 |
34842481 |
7.46 % |
25475481 |
5.67 % |
9367000 |
52.66 % |
| mq40 |
27185962 |
5.82 % |
26898891 |
5.99 % |
287071 |
1.61 % |
| q20,mq40 |
18654396 |
3.99 % |
18431613 |
4.10 % |
222783 |
1.25 % |
| q20,qd2,mq40 |
3541296 |
0.76 % |
3157085 |
0.70 % |
384211 |
2.16 % |
| qd2,mq40 |
255098 |
0.05 % |
235677 |
0.05 % |
19421 |
0.11 % |
| q20,qd2,fs60 |
7522 |
0.00 % |
0 |
0.00 % |
7522 |
0.04 % |
| qd2,fs60 |
6294 |
0.00 % |
0 |
0.00 % |
6294 |
0.04 % |
| fs60 |
3656 |
0.00 % |
0 |
0.00 % |
3656 |
0.02 % |
| qd2,fs60,mq40 |
2136 |
0.00 % |
0 |
0.00 % |
2136 |
0.01 % |
| fs60,mq40 |
974 |
0.00 % |
0 |
0.00 % |
974 |
0.01 % |
| q20,qd2,fs60,mq40 |
841 |
0.00 % |
0 |
0.00 % |
841 |
0.00 % |
| q20,fs60 |
11 |
0.00 % |
0 |
0.00 % |
11 |
0.00 % |
| q20,fs60,mq40 |
2 |
0.00 % |
0 |
0.00 % |
2 |
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 |
3600523 |
10.32 % |
| Transition |
G>A |
All |
10447417 |
29.95 % |
| Transition |
T>C |
All |
8245879 |
23.64 % |
| Transition |
C>T |
All |
9731119 |
27.90 % |
| Transversion |
A>C |
All |
257563 |
0.74 % |
| Transversion |
C>A |
All |
529367 |
1.52 % |
| Transversion |
T>G |
All |
265865 |
0.76 % |
| Transversion |
G>T |
All |
526735 |
1.51 % |
| Transversion |
A>T |
All |
437595 |
1.25 % |
| Transversion |
T>A |
All |
419083 |
1.20 % |
| Transversion |
C>G |
All |
217145 |
0.62 % |
| Transversion |
G>C |
All |
206319 |
0.59 % |
| |
|
|
|
|
| Transition |
A>G |
Passed |
383529 |
18.29 % |
| Transition |
G>A |
Passed |
339731 |
16.20 % |
| Transition |
T>C |
Passed |
443392 |
21.14 % |
| Transition |
C>T |
Passed |
338459 |
16.14 % |
| Transversion |
A>C |
Passed |
78255 |
3.73 % |
| Transversion |
C>A |
Passed |
72058 |
3.44 % |
| Transversion |
T>G |
Passed |
77924 |
3.72 % |
| Transversion |
G>T |
Passed |
72258 |
3.45 % |
| Transversion |
A>T |
Passed |
51264 |
2.44 % |
| Transversion |
T>A |
Passed |
50546 |
2.41 % |
| Transversion |
C>G |
Passed |
94562 |
4.51 % |
| Transversion |
G>C |
Passed |
95137 |
4.54 % |
| |
|
|
|
|
| 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 |
11.20 |
32024938 |
2859672 |
| Passed |
2.54 |
1505111 |
592004 |
| dbSNPAll |
0 |
0 |
0 |
| dbSNPPassed |
0 |
0 |
0 |