/cemt/variants/A36001_3_lane_gembs
BACK
SAMPLE A36001_3_lane_gembs
Variant counts
| Type |
Total |
Pass |
% |
| SNPs |
1168370526 |
904248604 |
77.39 % |
| Multiallelic |
0 |
0 |
0.00 % |
VCF Filtering Stats
| Type |
#Sites |
% |
#Non-Variant Sites |
% |
#Variant Sites |
% |
| All |
1168370526 |
100% |
1149991701 |
98.43 % |
18378825 |
1.57 % |
| |
|
|
|
|
|
|
| Passed |
906109918 |
77.55 % |
901515340 |
78.39 % |
4594578 |
0.51 % |
| Filtered |
262260608 |
22.45 % |
248476361 |
21.61 % |
13784247 |
1.52 % |
| |
|
|
|
|
|
|
| q20 |
218151023 |
83.18 % |
215442851 |
86.71 % |
2708172 |
19.65 % |
| q20,qd2 |
19600260 |
7.47 % |
9545034 |
3.84 % |
10055226 |
72.95 % |
| q20,mq40 |
12531936 |
4.78 % |
12258810 |
4.93 % |
273126 |
1.98 % |
| qd2 |
5984415 |
2.28 % |
5750585 |
2.31 % |
233830 |
1.70 % |
| q20,qd2,mq40 |
3308543 |
1.26 % |
3017614 |
1.21 % |
290929 |
2.11 % |
| mq40 |
2616064 |
1.00 % |
2405542 |
0.97 % |
210522 |
1.53 % |
| qd2,mq40 |
66210 |
0.03 % |
55925 |
0.02 % |
10285 |
0.07 % |
| qd2,fs60,mq40 |
892 |
0.00 % |
0 |
0.00 % |
892 |
0.01 % |
| qd2,fs60 |
464 |
0.00 % |
0 |
0.00 % |
464 |
0.00 % |
| fs60,mq40 |
300 |
0.00 % |
0 |
0.00 % |
300 |
0.00 % |
| fs60 |
260 |
0.00 % |
0 |
0.00 % |
260 |
0.00 % |
| q20,qd2,fs60 |
151 |
0.00 % |
0 |
0.00 % |
151 |
0.00 % |
| q20,qd2,fs60,mq40 |
89 |
0.00 % |
0 |
0.00 % |
89 |
0.00 % |
| q20,fs60 |
1 |
0.00 % |
0 |
0.00 % |
1 |
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 |
6136691 |
30.27 % |
| Transition |
G>A |
All |
1502146 |
7.41 % |
| Transition |
T>C |
All |
5717924 |
28.21 % |
| Transition |
C>T |
All |
1531185 |
7.55 % |
| Transversion |
A>C |
All |
428483 |
2.11 % |
| Transversion |
C>A |
All |
964374 |
4.76 % |
| Transversion |
T>G |
All |
445902 |
2.20 % |
| Transversion |
G>T |
All |
957569 |
4.72 % |
| Transversion |
A>T |
All |
931976 |
4.60 % |
| Transversion |
T>A |
All |
950070 |
4.69 % |
| Transversion |
C>G |
All |
359424 |
1.77 % |
| Transversion |
G>C |
All |
345623 |
1.70 % |
| |
|
|
|
|
| Transition |
A>G |
Passed |
669258 |
17.66 % |
| Transition |
G>A |
Passed |
576384 |
15.21 % |
| Transition |
T>C |
Passed |
654945 |
17.29 % |
| Transition |
C>T |
Passed |
579187 |
15.29 % |
| Transversion |
A>C |
Passed |
159246 |
4.20 % |
| Transversion |
C>A |
Passed |
183511 |
4.84 % |
| Transversion |
T>G |
Passed |
160212 |
4.23 % |
| Transversion |
G>T |
Passed |
181787 |
4.80 % |
| Transversion |
A>T |
Passed |
166531 |
4.40 % |
| Transversion |
T>A |
Passed |
166609 |
4.40 % |
| Transversion |
C>G |
Passed |
145496 |
3.84 % |
| Transversion |
G>C |
Passed |
145818 |
3.85 % |
| |
|
|
|
|
| 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 |
2.77 |
14887946 |
5383421 |
| Passed |
1.89 |
2479774 |
1309210 |
| dbSNPAll |
0 |
0 |
0 |
| dbSNPPassed |
0 |
0 |
0 |