/cemt/variants/A54767_3_lane_gembs
BACK
SAMPLE A54767_3_lane_gembs
Variant counts
| Type |
Total |
Pass |
% |
| SNPs |
1161690804 |
645423740 |
55.56 % |
| Multiallelic |
0 |
0 |
0.00 % |
VCF Filtering Stats
| Type |
#Sites |
% |
#Non-Variant Sites |
% |
#Variant Sites |
% |
| All |
1161690804 |
100% |
1138176285 |
97.98 % |
23514519 |
2.02 % |
| |
|
|
|
|
|
|
| Passed |
649166707 |
55.88 % |
643243077 |
56.52 % |
5923630 |
0.91 % |
| Filtered |
512524097 |
44.12 % |
494933208 |
43.48 % |
17590889 |
2.71 % |
| |
|
|
|
|
|
|
| q20 |
451723328 |
88.14 % |
446965998 |
90.31 % |
4757330 |
27.04 % |
| q20,qd2 |
26647698 |
5.20 % |
14667131 |
2.96 % |
11980567 |
68.11 % |
| qd2 |
17639865 |
3.44 % |
17402153 |
3.52 % |
237712 |
1.35 % |
| q20,mq40 |
11323062 |
2.21 % |
11119542 |
2.25 % |
203520 |
1.16 % |
| q20,qd2,mq40 |
3427536 |
0.67 % |
3209699 |
0.65 % |
217837 |
1.24 % |
| mq40 |
1662338 |
0.32 % |
1502647 |
0.30 % |
159691 |
0.91 % |
| qd2,mq40 |
78464 |
0.02 % |
66038 |
0.01 % |
12426 |
0.07 % |
| q20,qd2,fs60 |
6982 |
0.00 % |
0 |
0.00 % |
6982 |
0.04 % |
| qd2,fs60 |
6788 |
0.00 % |
0 |
0.00 % |
6788 |
0.04 % |
| fs60 |
5320 |
0.00 % |
0 |
0.00 % |
5320 |
0.03 % |
| qd2,fs60,mq40 |
1914 |
0.00 % |
0 |
0.00 % |
1914 |
0.01 % |
| fs60,mq40 |
465 |
0.00 % |
0 |
0.00 % |
465 |
0.00 % |
| q20,qd2,fs60,mq40 |
330 |
0.00 % |
0 |
0.00 % |
330 |
0.00 % |
| q20,fs60 |
6 |
0.00 % |
0 |
0.00 % |
6 |
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 |
8060244 |
30.46 % |
| Transition |
G>A |
All |
2358081 |
8.91 % |
| Transition |
T>C |
All |
6670106 |
25.21 % |
| Transition |
C>T |
All |
2402890 |
9.08 % |
| Transversion |
A>C |
All |
417508 |
1.58 % |
| Transversion |
C>A |
All |
1437982 |
5.43 % |
| Transversion |
T>G |
All |
494922 |
1.87 % |
| Transversion |
G>T |
All |
1375950 |
5.20 % |
| Transversion |
A>T |
All |
1184179 |
4.47 % |
| Transversion |
T>A |
All |
1254998 |
4.74 % |
| Transversion |
C>G |
All |
437474 |
1.65 % |
| Transversion |
G>C |
All |
367843 |
1.39 % |
| |
|
|
|
|
| Transition |
A>G |
Passed |
565196 |
19.23 % |
| Transition |
G>A |
Passed |
437712 |
14.90 % |
| Transition |
T>C |
Passed |
524302 |
17.84 % |
| Transition |
C>T |
Passed |
442272 |
15.05 % |
| Transversion |
A>C |
Passed |
119738 |
4.07 % |
| Transversion |
C>A |
Passed |
132162 |
4.50 % |
| Transversion |
T>G |
Passed |
121743 |
4.14 % |
| Transversion |
G>T |
Passed |
130198 |
4.43 % |
| Transversion |
A>T |
Passed |
116897 |
3.98 % |
| Transversion |
T>A |
Passed |
119061 |
4.05 % |
| Transversion |
C>G |
Passed |
115018 |
3.91 % |
| Transversion |
G>C |
Passed |
114251 |
3.89 % |
| |
|
|
|
|
| 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 |
2.80 |
19491321 |
6970856 |
| Passed |
2.03 |
1969482 |
969068 |
| dbSNPAll |
0 |
0 |
0 |
| dbSNPPassed |
0 |
0 |
0 |