/CEMT/variants/E00610_8_lane_gembs
BACK
SAMPLE E00610_8_lane_gembs
Variant counts
| Type |
Total |
Pass |
% |
| SNPs |
1238607791 |
633651227 |
51.16 % |
| Multiallelic |
0 |
0 |
0.00 % |
VCF Filtering Stats
| Type |
#Sites |
% |
#Non-Variant Sites |
% |
#Variant Sites |
% |
| All |
1238607791 |
100% |
1114619244 |
89.99 % |
123988547 |
10.01 % |
| |
|
|
|
|
|
|
| Passed |
665758989 |
53.75 % |
625598099 |
56.13 % |
40160890 |
6.03 % |
| Filtered |
572848802 |
46.25 % |
489021145 |
43.87 % |
83827657 |
12.59 % |
| |
|
|
|
|
|
|
| q20 |
456616316 |
79.71 % |
430172581 |
87.97 % |
26443735 |
31.55 % |
| q20,qd2 |
88786485 |
15.50 % |
33305775 |
6.81 % |
55480710 |
66.18 % |
| qd2 |
14335688 |
2.50 % |
13238154 |
2.71 % |
1097534 |
1.31 % |
| q20,mq40 |
8606884 |
1.50 % |
8349443 |
1.71 % |
257441 |
0.31 % |
| q20,qd2,mq40 |
3718426 |
0.65 % |
3521501 |
0.72 % |
196925 |
0.23 % |
| mq40 |
755295 |
0.13 % |
411343 |
0.08 % |
343952 |
0.41 % |
| qd2,mq40 |
29688 |
0.01 % |
22348 |
0.00 % |
7340 |
0.01 % |
| qd2,fs60 |
18 |
0.00 % |
0 |
0.00 % |
18 |
0.00 % |
| fs60 |
1 |
0.00 % |
0 |
0.00 % |
1 |
0.00 % |
| qd2,fs60,mq40 |
1 |
0.00 % |
0 |
0.00 % |
1 |
0.00 % |
| q20,fs60 |
0 |
0.00 % |
0 |
0.00 % |
0 |
0.00 % |
| q20,qd2,fs60 |
0 |
0.00 % |
0 |
0.00 % |
0 |
0.00 % |
| fs60,mq40 |
0 |
0.00 % |
0 |
0.00 % |
0 |
0.00 % |
| q20,fs60,mq40 |
0 |
0.00 % |
0 |
0.00 % |
0 |
0.00 % |
| q20,qd2,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 |
33560313 |
26.41 % |
| Transition |
G>A |
All |
7270719 |
5.72 % |
| Transition |
T>C |
All |
28018616 |
22.05 % |
| Transition |
C>T |
All |
7693871 |
6.06 % |
| Transversion |
A>C |
All |
4752721 |
3.74 % |
| Transversion |
C>A |
All |
6192178 |
4.87 % |
| Transversion |
T>G |
All |
5257516 |
4.14 % |
| Transversion |
G>T |
All |
6111487 |
4.81 % |
| Transversion |
A>T |
All |
10908141 |
8.59 % |
| Transversion |
T>A |
All |
11126374 |
8.76 % |
| Transversion |
C>G |
All |
3227120 |
2.54 % |
| Transversion |
G>C |
All |
2936646 |
2.31 % |
| |
|
|
|
|
| Transition |
A>G |
Passed |
2564436 |
30.08 % |
| Transition |
G>A |
Passed |
608536 |
7.14 % |
| Transition |
T>C |
Passed |
1977891 |
23.20 % |
| Transition |
C>T |
Passed |
650147 |
7.63 % |
| Transversion |
A>C |
Passed |
428824 |
5.03 % |
| Transversion |
C>A |
Passed |
232714 |
2.73 % |
| Transversion |
T>G |
Passed |
473285 |
5.55 % |
| Transversion |
G>T |
Passed |
244347 |
2.87 % |
| Transversion |
A>T |
Passed |
319342 |
3.75 % |
| Transversion |
T>A |
Passed |
303956 |
3.57 % |
| Transversion |
C>G |
Passed |
375398 |
4.40 % |
| Transversion |
G>C |
Passed |
346520 |
4.06 % |
| |
|
|
|
|
| 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 |
1.52 |
76543519 |
50512183 |
| Passed |
2.13 |
5801010 |
2724386 |
| dbSNPAll |
0 |
0 |
0 |
| dbSNPPassed |
0 |
0 |
0 |