/EXTERNAL Roadmap/variants/K006540_K006541_2_lane_gembs
BACK
SAMPLE K006540_K006541_2_lane_gembs
Variant counts
| Type |
Total |
Pass |
% |
| SNPs |
1165995524 |
763716863 |
65.50 % |
| Multiallelic |
0 |
0 |
0.00 % |
VCF Filtering Stats
| Type |
#Sites |
% |
#Non-Variant Sites |
% |
#Variant Sites |
% |
| All |
1165995524 |
100% |
1137675099 |
97.57 % |
28320425 |
2.43 % |
| |
|
|
|
|
|
|
| Passed |
768378865 |
65.90 % |
761259525 |
66.91 % |
7119340 |
0.93 % |
| Filtered |
397616659 |
34.10 % |
376415574 |
33.09 % |
21201085 |
2.76 % |
| |
|
|
|
|
|
|
| q20 |
311666295 |
78.38 % |
303615455 |
80.66 % |
8050840 |
37.97 % |
| q20,mq40 |
33673214 |
8.47 % |
33065972 |
8.78 % |
607242 |
2.86 % |
| mq40 |
26251144 |
6.60 % |
25507033 |
6.78 % |
744111 |
3.51 % |
| q20,qd2 |
17250334 |
4.34 % |
6472451 |
1.72 % |
10777883 |
50.84 % |
| q20,qd2,mq40 |
4346962 |
1.09 % |
3546997 |
0.94 % |
799965 |
3.77 % |
| qd2 |
4293314 |
1.08 % |
4103252 |
1.09 % |
190062 |
0.90 % |
| qd2,mq40 |
128745 |
0.03 % |
104414 |
0.03 % |
24331 |
0.11 % |
| fs60 |
3842 |
0.00 % |
0 |
0.00 % |
3842 |
0.02 % |
| fs60,mq40 |
1714 |
0.00 % |
0 |
0.00 % |
1714 |
0.01 % |
| q20,qd2,fs60 |
399 |
0.00 % |
0 |
0.00 % |
399 |
0.00 % |
| qd2,fs60 |
259 |
0.00 % |
0 |
0.00 % |
259 |
0.00 % |
| q20,qd2,fs60,mq40 |
196 |
0.00 % |
0 |
0.00 % |
196 |
0.00 % |
| q20,fs60 |
103 |
0.00 % |
0 |
0.00 % |
103 |
0.00 % |
| qd2,fs60,mq40 |
85 |
0.00 % |
0 |
0.00 % |
85 |
0.00 % |
| q20,fs60,mq40 |
53 |
0.00 % |
0 |
0.00 % |
53 |
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 |
9725393 |
31.95 % |
| Transition |
G>A |
All |
1665141 |
5.47 % |
| Transition |
T>C |
All |
11428392 |
37.54 % |
| Transition |
C>T |
All |
1537788 |
5.05 % |
| Transversion |
A>C |
All |
728499 |
2.39 % |
| Transversion |
C>A |
All |
751120 |
2.47 % |
| Transversion |
T>G |
All |
857794 |
2.82 % |
| Transversion |
G>T |
All |
766765 |
2.52 % |
| Transversion |
A>T |
All |
1008261 |
3.31 % |
| Transversion |
T>A |
All |
985771 |
3.24 % |
| Transversion |
C>G |
All |
531603 |
1.75 % |
| Transversion |
G>C |
All |
455838 |
1.50 % |
| |
|
|
|
|
| Transition |
A>G |
Passed |
690255 |
21.54 % |
| Transition |
G>A |
Passed |
423459 |
13.21 % |
| Transition |
T>C |
Passed |
741658 |
23.14 % |
| Transition |
C>T |
Passed |
429743 |
13.41 % |
| Transversion |
A>C |
Passed |
127033 |
3.96 % |
| Transversion |
C>A |
Passed |
107756 |
3.36 % |
| Transversion |
T>G |
Passed |
131310 |
4.10 % |
| Transversion |
G>T |
Passed |
108630 |
3.39 % |
| Transversion |
A>T |
Passed |
89595 |
2.80 % |
| Transversion |
T>A |
Passed |
89525 |
2.79 % |
| Transversion |
C>G |
Passed |
133837 |
4.18 % |
| Transversion |
G>C |
Passed |
132210 |
4.13 % |
| |
|
|
|
|
| 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 |
4.00 |
24356714 |
6085651 |
| Passed |
2.48 |
2285115 |
919896 |
| dbSNPAll |
0 |
0 |
0 |
| dbSNPPassed |
0 |
0 |
0 |