/CEMT/variants/A50431_A50429_4_lane_gembs
BACK
SAMPLE A50431_A50429_4_lane_gembs
Variant counts
| Type |
Total |
Pass |
% |
| SNPs |
1159695836 |
340915603 |
29.40 % |
| Multiallelic |
0 |
0 |
0.00 % |
VCF Filtering Stats
| Type |
#Sites |
% |
#Non-Variant Sites |
% |
#Variant Sites |
% |
| All |
1159695836 |
100% |
1130667793 |
97.50 % |
29028043 |
2.50 % |
| |
|
|
|
|
|
|
| Passed |
347148192 |
29.93 % |
339287794 |
30.01 % |
7860398 |
2.26 % |
| Filtered |
812547644 |
70.07 % |
791379999 |
69.99 % |
21167645 |
6.10 % |
| |
|
|
|
|
|
|
| q20 |
751406270 |
92.48 % |
744391918 |
94.06 % |
7014352 |
33.14 % |
| q20,qd2 |
43697181 |
5.38 % |
30017369 |
3.79 % |
13679812 |
64.63 % |
| q20,mq40 |
11197909 |
1.38 % |
11029804 |
1.39 % |
168105 |
0.79 % |
| q20,qd2,mq40 |
4262088 |
0.52 % |
4130390 |
0.52 % |
131698 |
0.62 % |
| qd2 |
1508812 |
0.19 % |
1455665 |
0.18 % |
53147 |
0.25 % |
| mq40 |
446261 |
0.05 % |
331614 |
0.04 % |
114647 |
0.54 % |
| qd2,mq40 |
28106 |
0.00 % |
23239 |
0.00 % |
4867 |
0.02 % |
| qd2,fs60,mq40 |
470 |
0.00 % |
0 |
0.00 % |
470 |
0.00 % |
| qd2,fs60 |
233 |
0.00 % |
0 |
0.00 % |
233 |
0.00 % |
| fs60,mq40 |
164 |
0.00 % |
0 |
0.00 % |
164 |
0.00 % |
| fs60 |
67 |
0.00 % |
0 |
0.00 % |
67 |
0.00 % |
| q20,qd2,fs60 |
46 |
0.00 % |
0 |
0.00 % |
46 |
0.00 % |
| q20,qd2,fs60,mq40 |
37 |
0.00 % |
0 |
0.00 % |
37 |
0.00 % |
| q20,fs60 |
0 |
0.00 % |
0 |
0.00 % |
0 |
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 |
8623922 |
27.47 % |
| Transition |
G>A |
All |
1755157 |
5.59 % |
| Transition |
T>C |
All |
7112586 |
22.66 % |
| Transition |
C>T |
All |
1858841 |
5.92 % |
| Transversion |
A>C |
All |
714743 |
2.28 % |
| Transversion |
C>A |
All |
2206495 |
7.03 % |
| Transversion |
T>G |
All |
876590 |
2.79 % |
| Transversion |
G>T |
All |
2108966 |
6.72 % |
| Transversion |
A>T |
All |
2411014 |
7.68 % |
| Transversion |
T>A |
All |
2542668 |
8.10 % |
| Transversion |
C>G |
All |
647576 |
2.06 % |
| Transversion |
G>C |
All |
530283 |
1.69 % |
| |
|
|
|
|
| Transition |
A>G |
Passed |
351644 |
17.24 % |
| Transition |
G>A |
Passed |
297161 |
14.57 % |
| Transition |
T>C |
Passed |
328873 |
16.12 % |
| Transition |
C>T |
Passed |
300630 |
14.74 % |
| Transversion |
A>C |
Passed |
89263 |
4.38 % |
| Transversion |
C>A |
Passed |
105936 |
5.19 % |
| Transversion |
T>G |
Passed |
92421 |
4.53 % |
| Transversion |
G>T |
Passed |
105244 |
5.16 % |
| Transversion |
A>T |
Passed |
101480 |
4.98 % |
| Transversion |
T>A |
Passed |
103026 |
5.05 % |
| Transversion |
C>G |
Passed |
82966 |
4.07 % |
| Transversion |
G>C |
Passed |
81081 |
3.98 % |
| |
|
|
|
|
| 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 |
1.61 |
19350506 |
12038335 |
| Passed |
1.68 |
1278308 |
761417 |
| dbSNPAll |
0 |
0 |
0 |
| dbSNPPassed |
0 |
0 |
0 |