/CEMT/variants/A36011_3_lane_gembs
BACK
SAMPLE A36011_3_lane_gembs
Variant counts
| Type |
Total |
Pass |
% |
| SNPs |
1158041053 |
728830913 |
62.94 % |
| Multiallelic |
0 |
0 |
0.00 % |
VCF Filtering Stats
| Type |
#Sites |
% |
#Non-Variant Sites |
% |
#Variant Sites |
% |
| All |
1158041053 |
100% |
1138593139 |
98.32 % |
19447914 |
1.68 % |
| |
|
|
|
|
|
|
| Passed |
731377455 |
63.16 % |
726205624 |
63.78 % |
5171831 |
0.71 % |
| Filtered |
426663598 |
36.84 % |
412387515 |
36.22 % |
14276083 |
1.95 % |
| |
|
|
|
|
|
|
| q20 |
380693506 |
89.23 % |
376928061 |
91.40 % |
3765445 |
26.38 % |
| q20,qd2 |
23600391 |
5.53 % |
13978578 |
3.39 % |
9621813 |
67.40 % |
| q20,mq40 |
11756427 |
2.76 % |
11525323 |
2.79 % |
231104 |
1.62 % |
| qd2 |
5058475 |
1.19 % |
4846799 |
1.18 % |
211676 |
1.48 % |
| q20,qd2,mq40 |
3272582 |
0.77 % |
3028622 |
0.73 % |
243960 |
1.71 % |
| mq40 |
2209223 |
0.52 % |
2024822 |
0.49 % |
184401 |
1.29 % |
| qd2,mq40 |
65496 |
0.02 % |
55310 |
0.01 % |
10186 |
0.07 % |
| q20,qd2,fs60 |
2312 |
0.00 % |
0 |
0.00 % |
2312 |
0.02 % |
| fs60 |
2154 |
0.00 % |
0 |
0.00 % |
2154 |
0.02 % |
| qd2,fs60 |
1422 |
0.00 % |
0 |
0.00 % |
1422 |
0.01 % |
| qd2,fs60,mq40 |
1133 |
0.00 % |
0 |
0.00 % |
1133 |
0.01 % |
| fs60,mq40 |
332 |
0.00 % |
0 |
0.00 % |
332 |
0.00 % |
| q20,qd2,fs60,mq40 |
134 |
0.00 % |
0 |
0.00 % |
134 |
0.00 % |
| q20,fs60 |
10 |
0.00 % |
0 |
0.00 % |
10 |
0.00 % |
| q20,fs60,mq40 |
1 |
0.00 % |
0 |
0.00 % |
1 |
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 |
5833516 |
27.03 % |
| Transition |
G>A |
All |
1882137 |
8.72 % |
| Transition |
T>C |
All |
5601512 |
25.95 % |
| Transition |
C>T |
All |
1896250 |
8.79 % |
| Transversion |
A>C |
All |
492577 |
2.28 % |
| Transversion |
C>A |
All |
1178160 |
5.46 % |
| Transversion |
T>G |
All |
501091 |
2.32 % |
| Transversion |
G>T |
All |
1175579 |
5.45 % |
| Transversion |
A>T |
All |
1081672 |
5.01 % |
| Transversion |
T>A |
All |
1096234 |
5.08 % |
| Transversion |
C>G |
All |
427766 |
1.98 % |
| Transversion |
G>C |
All |
418385 |
1.94 % |
| |
|
|
|
|
| Transition |
A>G |
Passed |
608677 |
17.54 % |
| Transition |
G>A |
Passed |
540054 |
15.56 % |
| Transition |
T>C |
Passed |
605894 |
17.46 % |
| Transition |
C>T |
Passed |
541767 |
15.61 % |
| Transversion |
A>C |
Passed |
143625 |
4.14 % |
| Transversion |
C>A |
Passed |
160844 |
4.63 % |
| Transversion |
T>G |
Passed |
143749 |
4.14 % |
| Transversion |
G>T |
Passed |
159747 |
4.60 % |
| Transversion |
A>T |
Passed |
148148 |
4.27 % |
| Transversion |
T>A |
Passed |
150240 |
4.33 % |
| Transversion |
C>G |
Passed |
133965 |
3.86 % |
| Transversion |
G>C |
Passed |
134010 |
3.86 % |
| |
|
|
|
|
| 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 |
2.39 |
15213415 |
6371464 |
| Passed |
1.96 |
2296392 |
1174328 |
| dbSNPAll |
0 |
0 |
0 |
| dbSNPPassed |
0 |
0 |
0 |