/REMC/variants/A27342_5_lane_gembs
BACK
SAMPLE A27342_5_lane_gembs
Variant counts
| Type |
Total |
Pass |
% |
| SNPs |
1171316387 |
942970126 |
80.51 % |
| Multiallelic |
0 |
0 |
0.00 % |
VCF Filtering Stats
| Type |
#Sites |
% |
#Non-Variant Sites |
% |
#Variant Sites |
% |
| All |
1171316387 |
100% |
1142115993 |
97.51 % |
29200394 |
2.49 % |
| |
|
|
|
|
|
|
| Passed |
945741032 |
80.74 % |
939826167 |
82.29 % |
5914865 |
0.63 % |
| Filtered |
225575355 |
19.26 % |
202289826 |
17.71 % |
23285529 |
2.46 % |
| |
|
|
|
|
|
|
| q20 |
172116898 |
76.30 % |
169243839 |
83.66 % |
2873059 |
12.34 % |
| q20,qd2 |
27209708 |
12.06 % |
7715484 |
3.81 % |
19494224 |
83.72 % |
| q20,mq40 |
16454721 |
7.29 % |
16295125 |
8.06 % |
159596 |
0.69 % |
| mq40 |
4087994 |
1.81 % |
3799156 |
1.88 % |
288838 |
1.24 % |
| q20,qd2,mq40 |
3481723 |
1.54 % |
3277945 |
1.62 % |
203778 |
0.88 % |
| qd2 |
2181521 |
0.97 % |
1924975 |
0.95 % |
256546 |
1.10 % |
| qd2,mq40 |
42002 |
0.02 % |
33302 |
0.02 % |
8700 |
0.04 % |
| qd2,fs60,mq40 |
424 |
0.00 % |
0 |
0.00 % |
424 |
0.00 % |
| fs60,mq40 |
165 |
0.00 % |
0 |
0.00 % |
165 |
0.00 % |
| qd2,fs60 |
112 |
0.00 % |
0 |
0.00 % |
112 |
0.00 % |
| fs60 |
39 |
0.00 % |
0 |
0.00 % |
39 |
0.00 % |
| q20,qd2,fs60,mq40 |
37 |
0.00 % |
0 |
0.00 % |
37 |
0.00 % |
| q20,qd2,fs60 |
10 |
0.00 % |
0 |
0.00 % |
10 |
0.00 % |
| q20,fs60,mq40 |
1 |
0.00 % |
0 |
0.00 % |
1 |
0.00 % |
| q20,fs60 |
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 |
13949428 |
45.18 % |
| Transition |
G>A |
All |
1678816 |
5.44 % |
| Transition |
T>C |
All |
9216317 |
29.85 % |
| Transition |
C>T |
All |
1980415 |
6.41 % |
| Transversion |
A>C |
All |
279284 |
0.90 % |
| Transversion |
C>A |
All |
727376 |
2.36 % |
| Transversion |
T>G |
All |
413896 |
1.34 % |
| Transversion |
G>T |
All |
632461 |
2.05 % |
| Transversion |
A>T |
All |
627095 |
2.03 % |
| Transversion |
T>A |
All |
730909 |
2.37 % |
| Transversion |
C>G |
All |
368112 |
1.19 % |
| Transversion |
G>C |
All |
271881 |
0.88 % |
| |
|
|
|
|
| Transition |
A>G |
Passed |
1207969 |
29.02 % |
| Transition |
G>A |
Passed |
542988 |
13.04 % |
| Transition |
T>C |
Passed |
689046 |
16.55 % |
| Transition |
C>T |
Passed |
562639 |
13.52 % |
| Transversion |
A>C |
Passed |
144407 |
3.47 % |
| Transversion |
C>A |
Passed |
147913 |
3.55 % |
| Transversion |
T>G |
Passed |
153918 |
3.70 % |
| Transversion |
G>T |
Passed |
149166 |
3.58 % |
| Transversion |
A>T |
Passed |
131989 |
3.17 % |
| Transversion |
T>A |
Passed |
131958 |
3.17 % |
| Transversion |
C>G |
Passed |
153790 |
3.69 % |
| Transversion |
G>C |
Passed |
147237 |
3.54 % |
| |
|
|
|
|
| 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 |
6.62 |
26824976 |
4051014 |
| Passed |
2.59 |
3002642 |
1160378 |
| dbSNPAll |
0 |
0 |
0 |
| dbSNPPassed |
0 |
0 |
0 |