/EXTERNAL Roadmap/variants/K006524_1_lane_gembs
BACK
SAMPLE K006524_1_lane_gembs
Variant counts
| Type |
Total |
Pass |
% |
| SNPs |
1170115437 |
626885997 |
53.57 % |
| Multiallelic |
0 |
0 |
0.00 % |
VCF Filtering Stats
| Type |
#Sites |
% |
#Non-Variant Sites |
% |
#Variant Sites |
% |
| All |
1170115437 |
100% |
1137892670 |
97.25 % |
32222767 |
2.75 % |
| |
|
|
|
|
|
|
| Passed |
632100767 |
54.02 % |
624263085 |
54.86 % |
7837682 |
1.24 % |
| Filtered |
538014670 |
45.98 % |
513629585 |
45.14 % |
24385085 |
3.86 % |
| |
|
|
|
|
|
|
| q20 |
479873179 |
89.19 % |
471227470 |
91.74 % |
8645709 |
35.45 % |
| q20,qd2 |
25695303 |
4.78 % |
10924790 |
2.13 % |
14770513 |
60.57 % |
| q20,mq40 |
20824433 |
3.87 % |
20600144 |
4.01 % |
224289 |
0.92 % |
| q20,qd2,mq40 |
4270120 |
0.79 % |
4033357 |
0.79 % |
236763 |
0.97 % |
| mq40 |
3885056 |
0.72 % |
3590133 |
0.70 % |
294923 |
1.21 % |
| qd2 |
3407785 |
0.63 % |
3207191 |
0.62 % |
200594 |
0.82 % |
| qd2,mq40 |
57028 |
0.01 % |
46500 |
0.01 % |
10528 |
0.04 % |
| qd2,fs60,mq40 |
714 |
0.00 % |
0 |
0.00 % |
714 |
0.00 % |
| fs60 |
337 |
0.00 % |
0 |
0.00 % |
337 |
0.00 % |
| fs60,mq40 |
267 |
0.00 % |
0 |
0.00 % |
267 |
0.00 % |
| qd2,fs60 |
248 |
0.00 % |
0 |
0.00 % |
248 |
0.00 % |
| q20,qd2,fs60 |
111 |
0.00 % |
0 |
0.00 % |
111 |
0.00 % |
| q20,qd2,fs60,mq40 |
88 |
0.00 % |
0 |
0.00 % |
88 |
0.00 % |
| q20,fs60 |
1 |
0.00 % |
0 |
0.00 % |
1 |
0.00 % |
| q20,fs60,mq40 |
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 |
16264036 |
47.61 % |
| Transition |
G>A |
All |
1482262 |
4.34 % |
| Transition |
T>C |
All |
8651160 |
25.33 % |
| Transition |
C>T |
All |
1882835 |
5.51 % |
| Transversion |
A>C |
All |
462485 |
1.35 % |
| Transversion |
C>A |
All |
971044 |
2.84 % |
| Transversion |
T>G |
All |
808018 |
2.37 % |
| Transversion |
G>T |
All |
746489 |
2.19 % |
| Transversion |
A>T |
All |
680310 |
1.99 % |
| Transversion |
T>A |
All |
929983 |
2.72 % |
| Transversion |
C>G |
All |
795564 |
2.33 % |
| Transversion |
G>C |
All |
486102 |
1.42 % |
| |
|
|
|
|
| Transition |
A>G |
Passed |
1070951 |
31.86 % |
| Transition |
G>A |
Passed |
401324 |
11.94 % |
| Transition |
T>C |
Passed |
542044 |
16.12 % |
| Transition |
C>T |
Passed |
421084 |
12.53 % |
| Transversion |
A>C |
Passed |
113378 |
3.37 % |
| Transversion |
C>A |
Passed |
117534 |
3.50 % |
| Transversion |
T>G |
Passed |
127722 |
3.80 % |
| Transversion |
G>T |
Passed |
118591 |
3.53 % |
| Transversion |
A>T |
Passed |
105731 |
3.15 % |
| Transversion |
T>A |
Passed |
105902 |
3.15 % |
| Transversion |
C>G |
Passed |
124225 |
3.70 % |
| Transversion |
G>C |
Passed |
113058 |
3.36 % |
| |
|
|
|
|
| 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 |
4.81 |
28280293 |
5879995 |
| Passed |
2.63 |
2435403 |
926141 |
| dbSNPAll |
0 |
0 |
0 |
| dbSNPPassed |
0 |
0 |
0 |