/EXTERNAL Roadmap/variants/K012814_1_lane_gembs
BACK
SAMPLE K012814_1_lane_gembs
Variant counts
| Type |
Total |
Pass |
% |
| SNPs |
1167973559 |
832446796 |
71.27 % |
| Multiallelic |
0 |
0 |
0.00 % |
VCF Filtering Stats
| Type |
#Sites |
% |
#Non-Variant Sites |
% |
#Variant Sites |
% |
| All |
1167973559 |
100% |
1140655936 |
97.66 % |
27317623 |
2.34 % |
| |
|
|
|
|
|
|
| Passed |
836127997 |
71.59 % |
829839890 |
72.75 % |
6288107 |
0.75 % |
| Filtered |
331845562 |
28.41 % |
310816046 |
27.25 % |
21029516 |
2.52 % |
| |
|
|
|
|
|
|
| q20 |
283678372 |
85.49 % |
280430927 |
90.22 % |
3247445 |
15.44 % |
| q20,qd2 |
24934078 |
7.51 % |
7791244 |
2.51 % |
17142834 |
81.52 % |
| q20,mq40 |
16076264 |
4.84 % |
15935591 |
5.13 % |
140673 |
0.67 % |
| q20,qd2,mq40 |
3616593 |
1.09 % |
3456413 |
1.11 % |
160180 |
0.76 % |
| mq40 |
2414705 |
0.73 % |
2171880 |
0.70 % |
242825 |
1.15 % |
| qd2 |
1087549 |
0.33 % |
1000393 |
0.32 % |
87156 |
0.41 % |
| qd2,mq40 |
37125 |
0.01 % |
29598 |
0.01 % |
7527 |
0.04 % |
| qd2,fs60,mq40 |
475 |
0.00 % |
0 |
0.00 % |
475 |
0.00 % |
| fs60,mq40 |
214 |
0.00 % |
0 |
0.00 % |
214 |
0.00 % |
| qd2,fs60 |
120 |
0.00 % |
0 |
0.00 % |
120 |
0.00 % |
| q20,qd2,fs60,mq40 |
35 |
0.00 % |
0 |
0.00 % |
35 |
0.00 % |
| fs60 |
24 |
0.00 % |
0 |
0.00 % |
24 |
0.00 % |
| q20,qd2,fs60 |
7 |
0.00 % |
0 |
0.00 % |
7 |
0.00 % |
| q20,fs60,mq40 |
1 |
0.00 % |
0 |
0.00 % |
1 |
0.00 % |
| q20,fs60 |
0 |
0.00 % |
0 |
0.00 % |
0 |
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 |
12261431 |
42.24 % |
| Transition |
G>A |
All |
1532281 |
5.28 % |
| Transition |
T>C |
All |
9242969 |
31.84 % |
| Transition |
C>T |
All |
1758148 |
6.06 % |
| Transversion |
A>C |
All |
273098 |
0.94 % |
| Transversion |
C>A |
All |
813718 |
2.80 % |
| Transversion |
T>G |
All |
396246 |
1.37 % |
| Transversion |
G>T |
All |
722209 |
2.49 % |
| Transversion |
A>T |
All |
643443 |
2.22 % |
| Transversion |
T>A |
All |
746615 |
2.57 % |
| Transversion |
C>G |
All |
364359 |
1.26 % |
| Transversion |
G>C |
All |
274240 |
0.94 % |
| |
|
|
|
|
| Transition |
A>G |
Passed |
807585 |
22.93 % |
| Transition |
G>A |
Passed |
497984 |
14.14 % |
| Transition |
T>C |
Passed |
603529 |
17.13 % |
| Transition |
C>T |
Passed |
510584 |
14.50 % |
| Transversion |
A>C |
Passed |
137814 |
3.91 % |
| Transversion |
C>A |
Passed |
142235 |
4.04 % |
| Transversion |
T>G |
Passed |
142903 |
4.06 % |
| Transversion |
G>T |
Passed |
143003 |
4.06 % |
| Transversion |
A>T |
Passed |
125836 |
3.57 % |
| Transversion |
T>A |
Passed |
126430 |
3.59 % |
| Transversion |
C>G |
Passed |
143828 |
4.08 % |
| Transversion |
G>C |
Passed |
140528 |
3.99 % |
| |
|
|
|
|
| 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 |
5.86 |
24794829 |
4233928 |
| Passed |
2.19 |
2419682 |
1102577 |
| dbSNPAll |
0 |
0 |
0 |
| dbSNPPassed |
0 |
0 |
0 |