/CEMT/variants/A83594_2_lane_gembs
BACK
SAMPLE A83594_2_lane_gembs
Variant counts
| Type |
Total |
Pass |
% |
| SNPs |
1175716455 |
846476803 |
72.00 % |
| Multiallelic |
0 |
0 |
0.00 % |
VCF Filtering Stats
| Type |
#Sites |
% |
#Non-Variant Sites |
% |
#Variant Sites |
% |
| All |
1175716455 |
100% |
1156335726 |
98.35 % |
19380729 |
1.65 % |
| |
|
|
|
|
|
|
| Passed |
850721186 |
72.36 % |
843827071 |
72.97 % |
6894115 |
0.81 % |
| Filtered |
324995269 |
27.64 % |
312508655 |
27.03 % |
12486614 |
1.47 % |
| |
|
|
|
|
|
|
| q20 |
294307230 |
90.56 % |
292619669 |
93.64 % |
1687561 |
13.51 % |
| q20,qd2 |
14658080 |
4.51 % |
4524979 |
1.45 % |
10133101 |
81.15 % |
| q20,mq40 |
9733635 |
3.00 % |
9641779 |
3.09 % |
91856 |
0.74 % |
| q20,qd2,mq40 |
2430338 |
0.75 % |
2313170 |
0.74 % |
117168 |
0.94 % |
| mq40 |
2053679 |
0.63 % |
1848510 |
0.59 % |
205169 |
1.64 % |
| qd2 |
1753611 |
0.54 % |
1515263 |
0.48 % |
238348 |
1.91 % |
| qd2,mq40 |
54546 |
0.02 % |
45285 |
0.01 % |
9261 |
0.07 % |
| qd2,fs60,mq40 |
1265 |
0.00 % |
0 |
0.00 % |
1265 |
0.01 % |
| qd2,fs60 |
1123 |
0.00 % |
0 |
0.00 % |
1123 |
0.01 % |
| fs60 |
821 |
0.00 % |
0 |
0.00 % |
821 |
0.01 % |
| q20,qd2,fs60 |
473 |
0.00 % |
0 |
0.00 % |
473 |
0.00 % |
| fs60,mq40 |
339 |
0.00 % |
0 |
0.00 % |
339 |
0.00 % |
| q20,qd2,fs60,mq40 |
129 |
0.00 % |
0 |
0.00 % |
129 |
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 |
7962678 |
37.68 % |
| Transition |
G>A |
All |
954273 |
4.52 % |
| Transition |
T>C |
All |
7981646 |
37.76 % |
| Transition |
C>T |
All |
962330 |
4.55 % |
| Transversion |
A>C |
All |
369122 |
1.75 % |
| Transversion |
C>A |
All |
507233 |
2.40 % |
| Transversion |
T>G |
All |
368881 |
1.75 % |
| Transversion |
G>T |
All |
493085 |
2.33 % |
| Transversion |
A>T |
All |
425579 |
2.01 % |
| Transversion |
T>A |
All |
436504 |
2.07 % |
| Transversion |
C>G |
All |
335978 |
1.59 % |
| Transversion |
G>C |
All |
337788 |
1.60 % |
| |
|
|
|
|
| Transition |
A>G |
Passed |
709920 |
19.37 % |
| Transition |
G>A |
Passed |
525005 |
14.32 % |
| Transition |
T>C |
Passed |
706727 |
19.28 % |
| Transition |
C>T |
Passed |
527028 |
14.38 % |
| Transversion |
A>C |
Passed |
154068 |
4.20 % |
| Transversion |
C>A |
Passed |
162012 |
4.42 % |
| Transversion |
T>G |
Passed |
154628 |
4.22 % |
| Transversion |
G>T |
Passed |
154950 |
4.23 % |
| Transversion |
A>T |
Passed |
138045 |
3.77 % |
| Transversion |
T>A |
Passed |
140809 |
3.84 % |
| Transversion |
C>G |
Passed |
146058 |
3.98 % |
| Transversion |
G>C |
Passed |
146212 |
3.99 % |
| |
|
|
|
|
| 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 |
5.46 |
17860927 |
3274170 |
| Passed |
2.06 |
2468680 |
1196782 |
| dbSNPAll |
0 |
0 |
0 |
| dbSNPPassed |
0 |
0 |
0 |