/CEMT/variants/A50428_A50426_4_lane_gembs
BACK
SAMPLE A50428_A50426_4_lane_gembs
Variant counts
| Type |
Total |
Pass |
% |
| SNPs |
1163543087 |
436457677 |
37.51 % |
| Multiallelic |
0 |
0 |
0.00 % |
VCF Filtering Stats
| Type |
#Sites |
% |
#Non-Variant Sites |
% |
#Variant Sites |
% |
| All |
1163543087 |
100% |
1128247789 |
96.97 % |
35295298 |
3.03 % |
| |
|
|
|
|
|
|
| Passed |
442910726 |
38.07 % |
434422766 |
38.50 % |
8487960 |
1.92 % |
| Filtered |
720632361 |
61.93 % |
693825023 |
61.50 % |
26807338 |
6.05 % |
| |
|
|
|
|
|
|
| q20 |
664873072 |
92.26 % |
657621713 |
94.78 % |
7251359 |
27.05 % |
| q20,qd2 |
39622649 |
5.50 % |
20603375 |
2.97 % |
19019274 |
70.95 % |
| q20,mq40 |
10980234 |
1.52 % |
10768910 |
1.55 % |
211324 |
0.79 % |
| q20,qd2,mq40 |
4040199 |
0.56 % |
3851246 |
0.56 % |
188953 |
0.70 % |
| qd2 |
700355 |
0.10 % |
680382 |
0.10 % |
19973 |
0.07 % |
| mq40 |
393231 |
0.05 % |
281576 |
0.04 % |
111655 |
0.42 % |
| qd2,mq40 |
21955 |
0.00 % |
17821 |
0.00 % |
4134 |
0.02 % |
| qd2,fs60,mq40 |
300 |
0.00 % |
0 |
0.00 % |
300 |
0.00 % |
| qd2,fs60 |
149 |
0.00 % |
0 |
0.00 % |
149 |
0.00 % |
| fs60,mq40 |
135 |
0.00 % |
0 |
0.00 % |
135 |
0.00 % |
| fs60 |
47 |
0.00 % |
0 |
0.00 % |
47 |
0.00 % |
| q20,qd2,fs60,mq40 |
21 |
0.00 % |
0 |
0.00 % |
21 |
0.00 % |
| q20,qd2,fs60 |
13 |
0.00 % |
0 |
0.00 % |
13 |
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 |
9071147 |
24.25 % |
| Transition |
G>A |
All |
2167051 |
5.79 % |
| Transition |
T>C |
All |
9081294 |
24.28 % |
| Transition |
C>T |
All |
2175394 |
5.82 % |
| Transversion |
A>C |
All |
845764 |
2.26 % |
| Transversion |
C>A |
All |
2900047 |
7.75 % |
| Transversion |
T>G |
All |
831479 |
2.22 % |
| Transversion |
G>T |
All |
2960556 |
7.92 % |
| Transversion |
A>T |
All |
3236537 |
8.65 % |
| Transversion |
T>A |
All |
3129682 |
8.37 % |
| Transversion |
C>G |
All |
500336 |
1.34 % |
| Transversion |
G>C |
All |
504111 |
1.35 % |
| |
|
|
|
|
| Transition |
A>G |
Passed |
410624 |
16.36 % |
| Transition |
G>A |
Passed |
365064 |
14.55 % |
| Transition |
T>C |
Passed |
410045 |
16.34 % |
| Transition |
C>T |
Passed |
366379 |
14.60 % |
| Transversion |
A>C |
Passed |
116731 |
4.65 % |
| Transversion |
C>A |
Passed |
133208 |
5.31 % |
| Transversion |
T>G |
Passed |
116316 |
4.64 % |
| Transversion |
G>T |
Passed |
133729 |
5.33 % |
| Transversion |
A>T |
Passed |
125975 |
5.02 % |
| Transversion |
T>A |
Passed |
126055 |
5.02 % |
| Transversion |
C>G |
Passed |
102339 |
4.08 % |
| Transversion |
G>C |
Passed |
102887 |
4.10 % |
| |
|
|
|
|
| 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 |
1.51 |
22494886 |
14908512 |
| Passed |
1.62 |
1552112 |
957240 |
| dbSNPAll |
0 |
0 |
0 |
| dbSNPPassed |
0 |
0 |
0 |