/cemt/variants/A36016_3_lane_gembs
BACK
SAMPLE A36016_3_lane_gembs
Variant counts
| Type |
Total |
Pass |
% |
| SNPs |
1167625554 |
884302265 |
75.74 % |
| Multiallelic |
0 |
0 |
0.00 % |
VCF Filtering Stats
| Type |
#Sites |
% |
#Non-Variant Sites |
% |
#Variant Sites |
% |
| All |
1167625554 |
100% |
1149588578 |
98.46 % |
18036976 |
1.54 % |
| |
|
|
|
|
|
|
| Passed |
886288192 |
75.91 % |
881654873 |
76.69 % |
4633319 |
0.52 % |
| Filtered |
281337362 |
24.09 % |
267933705 |
23.31 % |
13403657 |
1.51 % |
| |
|
|
|
|
|
|
| q20 |
237676335 |
84.48 % |
234967223 |
87.70 % |
2709112 |
20.21 % |
| q20,qd2 |
19646758 |
6.98 % |
9935851 |
3.71 % |
9710907 |
72.45 % |
| q20,mq40 |
12204259 |
4.34 % |
11946749 |
4.46 % |
257510 |
1.92 % |
| qd2 |
5877153 |
2.09 % |
5653010 |
2.11 % |
224143 |
1.67 % |
| q20,qd2,mq40 |
3273671 |
1.16 % |
2997562 |
1.12 % |
276109 |
2.06 % |
| mq40 |
2582584 |
0.92 % |
2372026 |
0.89 % |
210558 |
1.57 % |
| qd2,mq40 |
72390 |
0.03 % |
61284 |
0.02 % |
11106 |
0.08 % |
| qd2,fs60,mq40 |
1222 |
0.00 % |
0 |
0.00 % |
1222 |
0.01 % |
| qd2,fs60 |
939 |
0.00 % |
0 |
0.00 % |
939 |
0.01 % |
| fs60 |
924 |
0.00 % |
0 |
0.00 % |
924 |
0.01 % |
| q20,qd2,fs60 |
644 |
0.00 % |
0 |
0.00 % |
644 |
0.00 % |
| fs60,mq40 |
372 |
0.00 % |
0 |
0.00 % |
372 |
0.00 % |
| q20,qd2,fs60,mq40 |
108 |
0.00 % |
0 |
0.00 % |
108 |
0.00 % |
| q20,fs60,mq40 |
3 |
0.00 % |
0 |
0.00 % |
3 |
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 |
6005946 |
30.12 % |
| Transition |
G>A |
All |
1603041 |
8.04 % |
| Transition |
T>C |
All |
5629738 |
28.23 % |
| Transition |
C>T |
All |
1625704 |
8.15 % |
| Transversion |
A>C |
All |
387299 |
1.94 % |
| Transversion |
C>A |
All |
939203 |
4.71 % |
| Transversion |
T>G |
All |
406825 |
2.04 % |
| Transversion |
G>T |
All |
932199 |
4.67 % |
| Transversion |
A>T |
All |
854455 |
4.28 % |
| Transversion |
T>A |
All |
875975 |
4.39 % |
| Transversion |
C>G |
All |
346900 |
1.74 % |
| Transversion |
G>C |
All |
333322 |
1.67 % |
| |
|
|
|
|
| Transition |
A>G |
Passed |
657366 |
17.75 % |
| Transition |
G>A |
Passed |
574554 |
15.52 % |
| Transition |
T>C |
Passed |
648741 |
17.52 % |
| Transition |
C>T |
Passed |
577613 |
15.60 % |
| Transversion |
A>C |
Passed |
150780 |
4.07 % |
| Transversion |
C>A |
Passed |
173361 |
4.68 % |
| Transversion |
T>G |
Passed |
151738 |
4.10 % |
| Transversion |
G>T |
Passed |
171328 |
4.63 % |
| Transversion |
A>T |
Passed |
155065 |
4.19 % |
| Transversion |
T>A |
Passed |
156999 |
4.24 % |
| Transversion |
C>G |
Passed |
142494 |
3.85 % |
| Transversion |
G>C |
Passed |
142662 |
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 |
2.93 |
14864429 |
5076178 |
| Passed |
1.98 |
2458274 |
1244427 |
| dbSNPAll |
0 |
0 |
0 |
| dbSNPPassed |
0 |
0 |
0 |