/CEMT/variants/E00611_8_lane_gembs
BACK
SAMPLE E00611_8_lane_gembs
Variant counts
| Type |
Total |
Pass |
% |
| SNPs |
1235682700 |
602593397 |
48.77 % |
| Multiallelic |
0 |
0 |
0.00 % |
VCF Filtering Stats
| Type |
#Sites |
% |
#Non-Variant Sites |
% |
#Variant Sites |
% |
| All |
1235682700 |
100% |
1111531727 |
89.95 % |
124150973 |
10.05 % |
| |
|
|
|
|
|
|
| Passed |
634313986 |
51.33 % |
595130430 |
53.54 % |
39183556 |
6.18 % |
| Filtered |
601368714 |
48.67 % |
516401297 |
46.46 % |
84967417 |
13.40 % |
| |
|
|
|
|
|
|
| q20 |
481679785 |
80.10 % |
455525703 |
88.21 % |
26154082 |
30.78 % |
| q20,qd2 |
92580434 |
15.39 % |
35519929 |
6.88 % |
57060505 |
67.16 % |
| qd2 |
14188015 |
2.36 % |
13229077 |
2.56 % |
958938 |
1.13 % |
| q20,mq40 |
8462778 |
1.41 % |
8212815 |
1.59 % |
249963 |
0.29 % |
| q20,qd2,mq40 |
3698905 |
0.62 % |
3498396 |
0.68 % |
200509 |
0.24 % |
| mq40 |
725731 |
0.12 % |
390459 |
0.08 % |
335272 |
0.39 % |
| qd2,mq40 |
32982 |
0.01 % |
24918 |
0.00 % |
8064 |
0.01 % |
| qd2,fs60 |
56 |
0.00 % |
0 |
0.00 % |
56 |
0.00 % |
| qd2,fs60,mq40 |
18 |
0.00 % |
0 |
0.00 % |
18 |
0.00 % |
| fs60,mq40 |
6 |
0.00 % |
0 |
0.00 % |
6 |
0.00 % |
| fs60 |
3 |
0.00 % |
0 |
0.00 % |
3 |
0.00 % |
| q20,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 % |
| 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 |
31674007 |
24.90 % |
| Transition |
G>A |
All |
7134001 |
5.61 % |
| Transition |
T>C |
All |
26150902 |
20.56 % |
| Transition |
C>T |
All |
7511462 |
5.91 % |
| Transversion |
A>C |
All |
4687897 |
3.69 % |
| Transversion |
C>A |
All |
7779770 |
6.12 % |
| Transversion |
T>G |
All |
5260839 |
4.14 % |
| Transversion |
G>T |
All |
7708313 |
6.06 % |
| Transversion |
A>T |
All |
11396613 |
8.96 % |
| Transversion |
T>A |
All |
11541199 |
9.07 % |
| Transversion |
C>G |
All |
3348632 |
2.63 % |
| Transversion |
G>C |
All |
3009114 |
2.37 % |
| |
|
|
|
|
| Transition |
A>G |
Passed |
2248699 |
28.43 % |
| Transition |
G>A |
Passed |
577564 |
7.30 % |
| Transition |
T>C |
Passed |
1729283 |
21.86 % |
| Transition |
C>T |
Passed |
614760 |
7.77 % |
| Transversion |
A>C |
Passed |
409896 |
5.18 % |
| Transversion |
C>A |
Passed |
249305 |
3.15 % |
| Transversion |
T>G |
Passed |
452131 |
5.72 % |
| Transversion |
G>T |
Passed |
263590 |
3.33 % |
| Transversion |
A>T |
Passed |
309638 |
3.91 % |
| Transversion |
T>A |
Passed |
294944 |
3.73 % |
| Transversion |
C>G |
Passed |
396855 |
5.02 % |
| Transversion |
G>C |
Passed |
363615 |
4.60 % |
| |
|
|
|
|
| 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 |
1.32 |
72470372 |
54732377 |
| Passed |
1.89 |
5170306 |
2739974 |
| dbSNPAll |
0 |
0 |
0 |
| dbSNPPassed |
0 |
0 |
0 |