/EXTERNAL Roadmap/variants/K006546_K006547_2_lane_gembs
BACK
SAMPLE K006546_K006547_2_lane_gembs
Variant counts
| Type |
Total |
Pass |
% |
| SNPs |
1166247072 |
797167885 |
68.35 % |
| Multiallelic |
0 |
0 |
0.00 % |
VCF Filtering Stats
| Type |
#Sites |
% |
#Non-Variant Sites |
% |
#Variant Sites |
% |
| All |
1166247072 |
100% |
1143210499 |
98.02 % |
23036573 |
1.98 % |
| |
|
|
|
|
|
|
| Passed |
801140244 |
68.69 % |
794859865 |
69.53 % |
6280379 |
0.78 % |
| Filtered |
365106828 |
31.31 % |
348350634 |
30.47 % |
16756194 |
2.09 % |
| |
|
|
|
|
|
|
| q20 |
273176473 |
74.82 % |
267551010 |
76.81 % |
5625463 |
33.57 % |
| mq40 |
35278601 |
9.66 % |
34500713 |
9.90 % |
777888 |
4.64 % |
| q20,mq40 |
34887295 |
9.56 % |
34331521 |
9.86 % |
555774 |
3.32 % |
| q20,qd2 |
13995717 |
3.83 % |
5274105 |
1.51 % |
8721612 |
52.05 % |
| q20,qd2,mq40 |
4338199 |
1.19 % |
3502960 |
1.01 % |
835239 |
4.98 % |
| qd2 |
3234343 |
0.89 % |
3037634 |
0.87 % |
196709 |
1.17 % |
| qd2,mq40 |
186752 |
0.05 % |
152691 |
0.04 % |
34061 |
0.20 % |
| fs60 |
5675 |
0.00 % |
0 |
0.00 % |
5675 |
0.03 % |
| fs60,mq40 |
2501 |
0.00 % |
0 |
0.00 % |
2501 |
0.01 % |
| q20,qd2,fs60 |
445 |
0.00 % |
0 |
0.00 % |
445 |
0.00 % |
| qd2,fs60 |
407 |
0.00 % |
0 |
0.00 % |
407 |
0.00 % |
| q20,qd2,fs60,mq40 |
176 |
0.00 % |
0 |
0.00 % |
176 |
0.00 % |
| q20,fs60 |
111 |
0.00 % |
0 |
0.00 % |
111 |
0.00 % |
| qd2,fs60,mq40 |
102 |
0.00 % |
0 |
0.00 % |
102 |
0.00 % |
| q20,fs60,mq40 |
31 |
0.00 % |
0 |
0.00 % |
31 |
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 |
8269344 |
33.04 % |
| Transition |
G>A |
All |
1383369 |
5.53 % |
| Transition |
T>C |
All |
9312275 |
37.21 % |
| Transition |
C>T |
All |
1273212 |
5.09 % |
| Transversion |
A>C |
All |
551565 |
2.20 % |
| Transversion |
C>A |
All |
600045 |
2.40 % |
| Transversion |
T>G |
All |
659549 |
2.64 % |
| Transversion |
G>T |
All |
611307 |
2.44 % |
| Transversion |
A>T |
All |
791027 |
3.16 % |
| Transversion |
T>A |
All |
801484 |
3.20 % |
| Transversion |
C>G |
All |
414228 |
1.66 % |
| Transversion |
G>C |
All |
359368 |
1.44 % |
| |
|
|
|
|
| Transition |
A>G |
Passed |
657766 |
21.16 % |
| Transition |
G>A |
Passed |
420448 |
13.53 % |
| Transition |
T>C |
Passed |
701088 |
22.56 % |
| Transition |
C>T |
Passed |
425987 |
13.71 % |
| Transversion |
A>C |
Passed |
126038 |
4.06 % |
| Transversion |
C>A |
Passed |
105644 |
3.40 % |
| Transversion |
T>G |
Passed |
128198 |
4.12 % |
| Transversion |
G>T |
Passed |
106592 |
3.43 % |
| Transversion |
A>T |
Passed |
87499 |
2.82 % |
| Transversion |
T>A |
Passed |
87911 |
2.83 % |
| Transversion |
C>G |
Passed |
130929 |
4.21 % |
| Transversion |
G>C |
Passed |
129988 |
4.18 % |
| |
|
|
|
|
| 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 |
4.23 |
20238200 |
4788573 |
| Passed |
2.44 |
2205289 |
902799 |
| dbSNPAll |
0 |
0 |
0 |
| dbSNPPassed |
0 |
0 |
0 |