/EXTERNAL Roadmap/variants/K006525_K006526_K006527_K006528_K006529_5_lane_gembs
BACK
SAMPLE K006525_K006526_K006527_K006528_K006529_5_lane_gembs
Variant counts
| Type |
Total |
Pass |
% |
| SNPs |
1156417440 |
872945158 |
75.49 % |
| Multiallelic |
0 |
0 |
0.00 % |
VCF Filtering Stats
| Type |
#Sites |
% |
#Non-Variant Sites |
% |
#Variant Sites |
% |
| All |
1156417440 |
100% |
1141808181 |
98.74 % |
14609259 |
1.26 % |
| |
|
|
|
|
|
|
| Passed |
875282042 |
75.69 % |
870801363 |
76.27 % |
4480679 |
0.51 % |
| Filtered |
281135398 |
24.31 % |
271006818 |
23.73 % |
10128580 |
1.16 % |
| |
|
|
|
|
|
|
| q20 |
195112385 |
69.40 % |
192209035 |
70.92 % |
2903350 |
28.66 % |
| mq40 |
38813792 |
13.81 % |
38168931 |
14.08 % |
644861 |
6.37 % |
| q20,mq40 |
31237510 |
11.11 % |
30794092 |
11.36 % |
443418 |
4.38 % |
| q20,qd2 |
8819389 |
3.14 % |
3573630 |
1.32 % |
5245759 |
51.79 % |
| q20,qd2,mq40 |
4112216 |
1.46 % |
3450197 |
1.27 % |
662019 |
6.54 % |
| qd2 |
2814355 |
1.00 % |
2632859 |
0.97 % |
181496 |
1.79 % |
| qd2,mq40 |
212362 |
0.08 % |
178074 |
0.07 % |
34288 |
0.34 % |
| fs60 |
8623 |
0.00 % |
0 |
0.00 % |
8623 |
0.09 % |
| fs60,mq40 |
3125 |
0.00 % |
0 |
0.00 % |
3125 |
0.03 % |
| qd2,fs60 |
613 |
0.00 % |
0 |
0.00 % |
613 |
0.01 % |
| q20,qd2,fs60 |
572 |
0.00 % |
0 |
0.00 % |
572 |
0.01 % |
| q20,qd2,fs60,mq40 |
185 |
0.00 % |
0 |
0.00 % |
185 |
0.00 % |
| q20,fs60 |
133 |
0.00 % |
0 |
0.00 % |
133 |
0.00 % |
| qd2,fs60,mq40 |
101 |
0.00 % |
0 |
0.00 % |
101 |
0.00 % |
| q20,fs60,mq40 |
37 |
0.00 % |
0 |
0.00 % |
37 |
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 |
5849760 |
35.44 % |
| Transition |
G>A |
All |
1019811 |
6.18 % |
| Transition |
T>C |
All |
5981064 |
36.23 % |
| Transition |
C>T |
All |
964104 |
5.84 % |
| Transversion |
A>C |
All |
292360 |
1.77 % |
| Transversion |
C>A |
All |
389251 |
2.36 % |
| Transversion |
T>G |
All |
325794 |
1.97 % |
| Transversion |
G>T |
All |
389421 |
2.36 % |
| Transversion |
A>T |
All |
404763 |
2.45 % |
| Transversion |
T>A |
All |
406721 |
2.46 % |
| Transversion |
C>G |
All |
250287 |
1.52 % |
| Transversion |
G>C |
All |
233107 |
1.41 % |
| |
|
|
|
|
| Transition |
A>G |
Passed |
631495 |
20.82 % |
| Transition |
G>A |
Passed |
432617 |
14.26 % |
| Transition |
T>C |
Passed |
646611 |
21.31 % |
| Transition |
C>T |
Passed |
439587 |
14.49 % |
| Transversion |
A>C |
Passed |
119894 |
3.95 % |
| Transversion |
C>A |
Passed |
106929 |
3.52 % |
| Transversion |
T>G |
Passed |
121163 |
3.99 % |
| Transversion |
G>T |
Passed |
107741 |
3.55 % |
| Transversion |
A>T |
Passed |
88865 |
2.93 % |
| Transversion |
T>A |
Passed |
88860 |
2.93 % |
| Transversion |
C>G |
Passed |
124954 |
4.12 % |
| Transversion |
G>C |
Passed |
124881 |
4.12 % |
| |
|
|
|
|
| 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 |
5.13 |
13814739 |
2691704 |
| Passed |
2.43 |
2150310 |
883287 |
| dbSNPAll |
0 |
0 |
0 |
| dbSNPPassed |
0 |
0 |
0 |