/cemt/variants/K005716_0_lane_gembs
BACK
SAMPLE K005716_0_lane_gembs
Variant counts
| Type |
Total |
Pass |
% |
| SNPs |
1174064945 |
903900773 |
76.99 % |
| Multiallelic |
0 |
0 |
0.00 % |
VCF Filtering Stats
| Type |
#Sites |
% |
#Non-Variant Sites |
% |
#Variant Sites |
% |
| All |
1174064945 |
100% |
1148291695 |
97.80 % |
25773250 |
2.20 % |
| |
|
|
|
|
|
|
| Passed |
907696066 |
77.31 % |
900053603 |
78.38 % |
7642463 |
0.84 % |
| Filtered |
266368879 |
22.69 % |
248238092 |
21.62 % |
18130787 |
2.00 % |
| |
|
|
|
|
|
|
| q20 |
224318586 |
84.21 % |
222491647 |
89.63 % |
1826939 |
10.08 % |
| q20,qd2 |
22181374 |
8.33 % |
7168762 |
2.89 % |
15012612 |
82.80 % |
| q20,mq40 |
11568980 |
4.34 % |
11419071 |
4.60 % |
149909 |
0.83 % |
| q20,qd2,mq40 |
2804078 |
1.05 % |
2604553 |
1.05 % |
199525 |
1.10 % |
| mq40 |
2749335 |
1.03 % |
2429108 |
0.98 % |
320227 |
1.77 % |
| qd2 |
2696825 |
1.01 % |
2086405 |
0.84 % |
610420 |
3.37 % |
| qd2,mq40 |
48571 |
0.02 % |
38546 |
0.02 % |
10025 |
0.06 % |
| qd2,fs60,mq40 |
530 |
0.00 % |
0 |
0.00 % |
530 |
0.00 % |
| qd2,fs60 |
227 |
0.00 % |
0 |
0.00 % |
227 |
0.00 % |
| fs60,mq40 |
224 |
0.00 % |
0 |
0.00 % |
224 |
0.00 % |
| fs60 |
75 |
0.00 % |
0 |
0.00 % |
75 |
0.00 % |
| q20,qd2,fs60,mq40 |
58 |
0.00 % |
0 |
0.00 % |
58 |
0.00 % |
| q20,qd2,fs60 |
15 |
0.00 % |
0 |
0.00 % |
15 |
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 |
10050161 |
36.30 % |
| Transition |
G>A |
All |
1284422 |
4.64 % |
| Transition |
T>C |
All |
9553583 |
34.51 % |
| Transition |
C>T |
All |
1331676 |
4.81 % |
| Transversion |
A>C |
All |
400330 |
1.45 % |
| Transversion |
C>A |
All |
1124040 |
4.06 % |
| Transversion |
T>G |
All |
436402 |
1.58 % |
| Transversion |
G>T |
All |
1093140 |
3.95 % |
| Transversion |
A>T |
All |
674522 |
2.44 % |
| Transversion |
T>A |
All |
698141 |
2.52 % |
| Transversion |
C>G |
All |
537442 |
1.94 % |
| Transversion |
G>C |
All |
503420 |
1.82 % |
| |
|
|
|
|
| Transition |
A>G |
Passed |
1310643 |
26.25 % |
| Transition |
G>A |
Passed |
581680 |
11.65 % |
| Transition |
T>C |
Passed |
1099357 |
22.02 % |
| Transition |
C>T |
Passed |
574427 |
11.50 % |
| Transversion |
A>C |
Passed |
169021 |
3.38 % |
| Transversion |
C>A |
Passed |
217290 |
4.35 % |
| Transversion |
T>G |
Passed |
174512 |
3.49 % |
| Transversion |
G>T |
Passed |
193471 |
3.87 % |
| Transversion |
A>T |
Passed |
155142 |
3.11 % |
| Transversion |
T>A |
Passed |
161081 |
3.23 % |
| Transversion |
C>G |
Passed |
181387 |
3.63 % |
| Transversion |
G>C |
Passed |
175433 |
3.51 % |
| |
|
|
|
|
| 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 |
4.06 |
22219842 |
5467437 |
| Passed |
2.50 |
3566107 |
1427337 |
| dbSNPAll |
0 |
0 |
0 |
| dbSNPPassed |
0 |
0 |
0 |