/EXTERNAL Roadmap/variants/K006521_K006522_K006523_3_lane_gembs
BACK
SAMPLE K006521_K006522_K006523_3_lane_gembs
Variant counts
| Type |
Total |
Pass |
% |
| SNPs |
1158184057 |
1079288563 |
93.19 % |
| Multiallelic |
0 |
0 |
0.00 % |
VCF Filtering Stats
| Type |
#Sites |
% |
#Non-Variant Sites |
% |
#Variant Sites |
% |
| All |
1158184057 |
100% |
1149398371 |
99.24 % |
8785686 |
0.76 % |
| |
|
|
|
|
|
|
| Passed |
1079403618 |
93.20 % |
1074839338 |
93.51 % |
4564280 |
0.42 % |
| Filtered |
78780439 |
6.80 % |
74559033 |
6.49 % |
4221406 |
0.39 % |
| |
|
|
|
|
|
|
| mq40 |
47182480 |
59.89 % |
46556101 |
62.44 % |
626379 |
14.84 % |
| q20,mq40 |
15705872 |
19.94 % |
15472888 |
20.75 % |
232984 |
5.52 % |
| q20 |
8591043 |
10.91 % |
8390476 |
11.25 % |
200567 |
4.75 % |
| q20,qd2 |
2344162 |
2.98 % |
676462 |
0.91 % |
1667700 |
39.51 % |
| q20,qd2,mq40 |
2328201 |
2.96 % |
1674188 |
2.25 % |
654013 |
15.49 % |
| qd2 |
2000951 |
2.54 % |
1458599 |
1.96 % |
542352 |
12.85 % |
| qd2,mq40 |
420529 |
0.53 % |
330319 |
0.44 % |
90210 |
2.14 % |
| fs60 |
80912 |
0.10 % |
0 |
0.00 % |
80912 |
1.92 % |
| q20,qd2,fs60 |
80437 |
0.10 % |
0 |
0.00 % |
80437 |
1.91 % |
| fs60,mq40 |
19213 |
0.02 % |
0 |
0.00 % |
19213 |
0.46 % |
| q20,fs60 |
16224 |
0.02 % |
0 |
0.00 % |
16224 |
0.38 % |
| qd2,fs60 |
7045 |
0.01 % |
0 |
0.00 % |
7045 |
0.17 % |
| qd2,fs60,mq40 |
1827 |
0.00 % |
0 |
0.00 % |
1827 |
0.04 % |
| q20,qd2,fs60,mq40 |
1371 |
0.00 % |
0 |
0.00 % |
1371 |
0.03 % |
| q20,fs60,mq40 |
172 |
0.00 % |
0 |
0.00 % |
172 |
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 |
2172634 |
22.52 % |
| Transition |
G>A |
All |
1200735 |
12.45 % |
| Transition |
T>C |
All |
2165348 |
22.45 % |
| Transition |
C>T |
All |
1215027 |
12.60 % |
| Transversion |
A>C |
All |
287108 |
2.98 % |
| Transversion |
C>A |
All |
437076 |
4.53 % |
| Transversion |
T>G |
All |
287328 |
2.98 % |
| Transversion |
G>T |
All |
450362 |
4.67 % |
| Transversion |
A>T |
All |
443117 |
4.59 % |
| Transversion |
T>A |
All |
421406 |
4.37 % |
| Transversion |
C>G |
All |
281172 |
2.92 % |
| Transversion |
G>C |
All |
284167 |
2.95 % |
| |
|
|
|
|
| Transition |
A>G |
Passed |
896204 |
17.76 % |
| Transition |
G>A |
Passed |
786507 |
15.58 % |
| Transition |
T>C |
Passed |
909975 |
18.03 % |
| Transition |
C>T |
Passed |
801047 |
15.87 % |
| Transversion |
A>C |
Passed |
212142 |
4.20 % |
| Transversion |
C>A |
Passed |
212514 |
4.21 % |
| Transversion |
T>G |
Passed |
210338 |
4.17 % |
| Transversion |
G>T |
Passed |
212534 |
4.21 % |
| Transversion |
A>T |
Passed |
193378 |
3.83 % |
| Transversion |
T>A |
Passed |
191790 |
3.80 % |
| Transversion |
C>G |
Passed |
209585 |
4.15 % |
| Transversion |
G>C |
Passed |
211275 |
4.19 % |
| |
|
|
|
|
| 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 |
2.34 |
6753744 |
2891736 |
| Passed |
2.05 |
3393733 |
1653556 |
| dbSNPAll |
0 |
0 |
0 |
| dbSNPPassed |
0 |
0 |
0 |