/cemt/variants/A36000_3_lane_gembs
BACK
SAMPLE A36000_3_lane_gembs
Variant counts
| Type |
Total |
Pass |
% |
| SNPs |
1160945321 |
950741284 |
81.89 % |
| Multiallelic |
0 |
0 |
0.00 % |
VCF Filtering Stats
| Type |
#Sites |
% |
#Non-Variant Sites |
% |
#Variant Sites |
% |
| All |
1160945321 |
100% |
1145359225 |
98.66 % |
15586096 |
1.34 % |
| |
|
|
|
|
|
|
| Passed |
952140853 |
82.01 % |
948067646 |
82.77 % |
4073207 |
0.43 % |
| Filtered |
208804468 |
17.99 % |
197291579 |
17.23 % |
11512889 |
1.21 % |
| |
|
|
|
|
|
|
| q20 |
168520302 |
80.71 % |
166448891 |
84.37 % |
2071411 |
17.99 % |
| q20,qd2 |
16350473 |
7.83 % |
7886550 |
4.00 % |
8463923 |
73.52 % |
| q20,mq40 |
12042251 |
5.77 % |
11793400 |
5.98 % |
248851 |
2.16 % |
| qd2 |
5764405 |
2.76 % |
5537707 |
2.81 % |
226698 |
1.97 % |
| q20,qd2,mq40 |
3139275 |
1.50 % |
2859519 |
1.45 % |
279756 |
2.43 % |
| mq40 |
2920297 |
1.40 % |
2711274 |
1.37 % |
209023 |
1.82 % |
| qd2,mq40 |
65159 |
0.03 % |
54238 |
0.03 % |
10921 |
0.09 % |
| qd2,fs60,mq40 |
858 |
0.00 % |
0 |
0.00 % |
858 |
0.01 % |
| qd2,fs60 |
502 |
0.00 % |
0 |
0.00 % |
502 |
0.00 % |
| fs60 |
356 |
0.00 % |
0 |
0.00 % |
356 |
0.00 % |
| fs60,mq40 |
283 |
0.00 % |
0 |
0.00 % |
283 |
0.00 % |
| q20,qd2,fs60 |
209 |
0.00 % |
0 |
0.00 % |
209 |
0.00 % |
| q20,qd2,fs60,mq40 |
92 |
0.00 % |
0 |
0.00 % |
92 |
0.00 % |
| q20,fs60 |
3 |
0.00 % |
0 |
0.00 % |
3 |
0.00 % |
| q20,fs60,mq40 |
3 |
0.00 % |
0 |
0.00 % |
3 |
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 |
5254483 |
30.16 % |
| Transition |
G>A |
All |
1368386 |
7.85 % |
| Transition |
T>C |
All |
4965138 |
28.50 % |
| Transition |
C>T |
All |
1399395 |
8.03 % |
| Transversion |
A>C |
All |
360684 |
2.07 % |
| Transversion |
C>A |
All |
760190 |
4.36 % |
| Transversion |
T>G |
All |
375952 |
2.16 % |
| Transversion |
G>T |
All |
759535 |
4.36 % |
| Transversion |
A>T |
All |
776831 |
4.46 % |
| Transversion |
T>A |
All |
788879 |
4.53 % |
| Transversion |
C>G |
All |
310413 |
1.78 % |
| Transversion |
G>C |
All |
301163 |
1.73 % |
| |
|
|
|
|
| Transition |
A>G |
Passed |
671273 |
17.77 % |
| Transition |
G>A |
Passed |
587833 |
15.56 % |
| Transition |
T>C |
Passed |
663914 |
17.57 % |
| Transition |
C>T |
Passed |
589295 |
15.60 % |
| Transversion |
A>C |
Passed |
157827 |
4.18 % |
| Transversion |
C>A |
Passed |
170248 |
4.51 % |
| Transversion |
T>G |
Passed |
158990 |
4.21 % |
| Transversion |
G>T |
Passed |
170210 |
4.50 % |
| Transversion |
A>T |
Passed |
155198 |
4.11 % |
| Transversion |
T>A |
Passed |
156331 |
4.14 % |
| Transversion |
C>G |
Passed |
148615 |
3.93 % |
| Transversion |
G>C |
Passed |
148886 |
3.94 % |
| |
|
|
|
|
| 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 |
12987402 |
4433647 |
| Passed |
1.98 |
2512315 |
1266305 |
| dbSNPAll |
0 |
0 |
0 |
| dbSNPPassed |
0 |
0 |
0 |