/cemt/variants/K005713_0_lane_gembs
BACK
SAMPLE K005713_0_lane_gembs
Variant counts
| Type |
Total |
Pass |
% |
| SNPs |
1165814747 |
578199385 |
49.60 % |
| Multiallelic |
0 |
0 |
0.00 % |
VCF Filtering Stats
| Type |
#Sites |
% |
#Non-Variant Sites |
% |
#Variant Sites |
% |
| All |
1165814747 |
100% |
1139802938 |
97.77 % |
26011809 |
2.23 % |
| |
|
|
|
|
|
|
| Passed |
583008966 |
50.01 % |
575488750 |
50.49 % |
7520216 |
1.29 % |
| Filtered |
582805781 |
49.99 % |
564314188 |
49.51 % |
18491593 |
3.17 % |
| |
|
|
|
|
|
|
| q20 |
534541978 |
91.72 % |
529390885 |
93.81 % |
5151093 |
27.86 % |
| q20,qd2 |
27681111 |
4.75 % |
15233750 |
2.70 % |
12447361 |
67.31 % |
| q20,mq40 |
13058301 |
2.24 % |
12863250 |
2.28 % |
195051 |
1.05 % |
| q20,qd2,mq40 |
3621841 |
0.62 % |
3435038 |
0.61 % |
186803 |
1.01 % |
| qd2 |
2027239 |
0.35 % |
1760292 |
0.31 % |
266947 |
1.44 % |
| mq40 |
1835878 |
0.32 % |
1600056 |
0.28 % |
235822 |
1.28 % |
| qd2,mq40 |
38257 |
0.01 % |
30917 |
0.01 % |
7340 |
0.04 % |
| qd2,fs60,mq40 |
499 |
0.00 % |
0 |
0.00 % |
499 |
0.00 % |
| qd2,fs60 |
245 |
0.00 % |
0 |
0.00 % |
245 |
0.00 % |
| fs60,mq40 |
160 |
0.00 % |
0 |
0.00 % |
160 |
0.00 % |
| q20,qd2,fs60,mq40 |
95 |
0.00 % |
0 |
0.00 % |
95 |
0.00 % |
| q20,qd2,fs60 |
92 |
0.00 % |
0 |
0.00 % |
92 |
0.00 % |
| fs60 |
85 |
0.00 % |
0 |
0.00 % |
85 |
0.00 % |
| q20,fs60 |
0 |
0.00 % |
0 |
0.00 % |
0 |
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 |
9219330 |
32.90 % |
| Transition |
G>A |
All |
1050798 |
3.75 % |
| Transition |
T>C |
All |
7669527 |
27.37 % |
| Transition |
C>T |
All |
1157036 |
4.13 % |
| Transversion |
A>C |
All |
1112028 |
3.97 % |
| Transversion |
C>A |
All |
1377319 |
4.91 % |
| Transversion |
T>G |
All |
1213578 |
4.33 % |
| Transversion |
G>T |
All |
1264195 |
4.51 % |
| Transversion |
A>T |
All |
896033 |
3.20 % |
| Transversion |
T>A |
All |
1040876 |
3.71 % |
| Transversion |
C>G |
All |
1053974 |
3.76 % |
| Transversion |
G>C |
All |
969485 |
3.46 % |
| |
|
|
|
|
| Transition |
A>G |
Passed |
720983 |
21.23 % |
| Transition |
G>A |
Passed |
412561 |
12.15 % |
| Transition |
T>C |
Passed |
741179 |
21.83 % |
| Transition |
C>T |
Passed |
431950 |
12.72 % |
| Transversion |
A>C |
Passed |
139512 |
4.11 % |
| Transversion |
C>A |
Passed |
144179 |
4.25 % |
| Transversion |
T>G |
Passed |
149737 |
4.41 % |
| Transversion |
G>T |
Passed |
143130 |
4.21 % |
| Transversion |
A>T |
Passed |
125487 |
3.70 % |
| Transversion |
T>A |
Passed |
125604 |
3.70 % |
| Transversion |
C>G |
Passed |
134116 |
3.95 % |
| Transversion |
G>C |
Passed |
127298 |
3.75 % |
| |
|
|
|
|
| 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 |
2.14 |
19096691 |
8927488 |
| Passed |
2.12 |
2306673 |
1089063 |
| dbSNPAll |
0 |
0 |
0 |
| dbSNPPassed |
0 |
0 |
0 |