/EXTERNAL Roadmap/variants/K012812_1_lane_gembs
BACK
SAMPLE K012812_1_lane_gembs
Variant counts
| Type |
Total |
Pass |
% |
| SNPs |
1170155955 |
842124153 |
71.97 % |
| Multiallelic |
0 |
0 |
0.00 % |
VCF Filtering Stats
| Type |
#Sites |
% |
#Non-Variant Sites |
% |
#Variant Sites |
% |
| All |
1170155955 |
100% |
1139044801 |
97.34 % |
31111154 |
2.66 % |
| |
|
|
|
|
|
|
| Passed |
846439604 |
72.34 % |
839267775 |
73.68 % |
7171829 |
0.85 % |
| Filtered |
323716351 |
27.66 % |
299777026 |
26.32 % |
23939325 |
2.83 % |
| |
|
|
|
|
|
|
| q20 |
271257648 |
83.79 % |
267735205 |
89.31 % |
3522443 |
14.71 % |
| q20,qd2 |
28724740 |
8.87 % |
9056111 |
3.02 % |
19668629 |
82.16 % |
| q20,mq40 |
15798461 |
4.88 % |
15653059 |
5.22 % |
145402 |
0.61 % |
| q20,qd2,mq40 |
3480833 |
1.08 % |
3308212 |
1.10 % |
172621 |
0.72 % |
| mq40 |
2544166 |
0.79 % |
2272287 |
0.76 % |
271879 |
1.14 % |
| qd2 |
1868691 |
0.58 % |
1719460 |
0.57 % |
149231 |
0.62 % |
| qd2,mq40 |
40866 |
0.01 % |
32692 |
0.01 % |
8174 |
0.03 % |
| qd2,fs60,mq40 |
480 |
0.00 % |
0 |
0.00 % |
480 |
0.00 % |
| fs60,mq40 |
260 |
0.00 % |
0 |
0.00 % |
260 |
0.00 % |
| qd2,fs60 |
134 |
0.00 % |
0 |
0.00 % |
134 |
0.00 % |
| q20,qd2,fs60,mq40 |
39 |
0.00 % |
0 |
0.00 % |
39 |
0.00 % |
| fs60 |
24 |
0.00 % |
0 |
0.00 % |
24 |
0.00 % |
| q20,qd2,fs60 |
6 |
0.00 % |
0 |
0.00 % |
6 |
0.00 % |
| q20,fs60,mq40 |
3 |
0.00 % |
0 |
0.00 % |
3 |
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 |
13352950 |
40.67 % |
| Transition |
G>A |
All |
2121368 |
6.46 % |
| Transition |
T>C |
All |
9967174 |
30.36 % |
| Transition |
C>T |
All |
2245010 |
6.84 % |
| Transversion |
A>C |
All |
327298 |
1.00 % |
| Transversion |
C>A |
All |
941075 |
2.87 % |
| Transversion |
T>G |
All |
454246 |
1.38 % |
| Transversion |
G>T |
All |
862284 |
2.63 % |
| Transversion |
A>T |
All |
870734 |
2.65 % |
| Transversion |
T>A |
All |
953691 |
2.91 % |
| Transversion |
C>G |
All |
412930 |
1.26 % |
| Transversion |
G>C |
All |
320128 |
0.98 % |
| |
|
|
|
|
| Transition |
A>G |
Passed |
893995 |
23.73 % |
| Transition |
G>A |
Passed |
525942 |
13.96 % |
| Transition |
T>C |
Passed |
652409 |
17.31 % |
| Transition |
C>T |
Passed |
537859 |
14.27 % |
| Transversion |
A>C |
Passed |
144128 |
3.82 % |
| Transversion |
C>A |
Passed |
147708 |
3.92 % |
| Transversion |
T>G |
Passed |
150379 |
3.99 % |
| Transversion |
G>T |
Passed |
149224 |
3.96 % |
| Transversion |
A>T |
Passed |
135592 |
3.60 % |
| Transversion |
T>A |
Passed |
135468 |
3.60 % |
| Transversion |
C>G |
Passed |
149680 |
3.97 % |
| Transversion |
G>C |
Passed |
145697 |
3.87 % |
| |
|
|
|
|
| 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 |
5.38 |
27686502 |
5142386 |
| Passed |
2.25 |
2610205 |
1157876 |
| dbSNPAll |
0 |
0 |
0 |
| dbSNPPassed |
0 |
0 |
0 |