/cemt/variants/A36009_3_lane_gembs
BACK
SAMPLE A36009_3_lane_gembs
Variant counts
| Type |
Total |
Pass |
% |
| SNPs |
1159393790 |
867192682 |
74.80 % |
| Multiallelic |
0 |
0 |
0.00 % |
VCF Filtering Stats
| Type |
#Sites |
% |
#Non-Variant Sites |
% |
#Variant Sites |
% |
| All |
1159393790 |
100% |
1142845787 |
98.57 % |
16548003 |
1.43 % |
| |
|
|
|
|
|
|
| Passed |
868969448 |
74.95 % |
864640042 |
75.66 % |
4329406 |
0.50 % |
| Filtered |
290424342 |
25.05 % |
278205745 |
24.34 % |
12218597 |
1.41 % |
| |
|
|
|
|
|
|
| q20 |
249352561 |
85.86 % |
246704289 |
88.68 % |
2648272 |
21.67 % |
| q20,qd2 |
18241893 |
6.28 % |
9593029 |
3.45 % |
8648864 |
70.78 % |
| q20,mq40 |
11731227 |
4.04 % |
11485573 |
4.13 % |
245654 |
2.01 % |
| qd2 |
5346320 |
1.84 % |
5135396 |
1.85 % |
210924 |
1.73 % |
| q20,qd2,mq40 |
3131446 |
1.08 % |
2867296 |
1.03 % |
264150 |
2.16 % |
| mq40 |
2548862 |
0.88 % |
2363254 |
0.85 % |
185608 |
1.52 % |
| qd2,mq40 |
67410 |
0.02 % |
56908 |
0.02 % |
10502 |
0.09 % |
| fs60 |
1156 |
0.00 % |
0 |
0.00 % |
1156 |
0.01 % |
| qd2,fs60,mq40 |
1114 |
0.00 % |
0 |
0.00 % |
1114 |
0.01 % |
| q20,qd2,fs60 |
976 |
0.00 % |
0 |
0.00 % |
976 |
0.01 % |
| qd2,fs60 |
936 |
0.00 % |
0 |
0.00 % |
936 |
0.01 % |
| fs60,mq40 |
312 |
0.00 % |
0 |
0.00 % |
312 |
0.00 % |
| q20,qd2,fs60,mq40 |
126 |
0.00 % |
0 |
0.00 % |
126 |
0.00 % |
| q20,fs60 |
3 |
0.00 % |
0 |
0.00 % |
3 |
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 |
5284897 |
28.65 % |
| Transition |
G>A |
All |
1576074 |
8.54 % |
| Transition |
T>C |
All |
5155001 |
27.94 % |
| Transition |
C>T |
All |
1580907 |
8.57 % |
| Transversion |
A>C |
All |
392777 |
2.13 % |
| Transversion |
C>A |
All |
851479 |
4.62 % |
| Transversion |
T>G |
All |
401086 |
2.17 % |
| Transversion |
G>T |
All |
851266 |
4.61 % |
| Transversion |
A>T |
All |
839813 |
4.55 % |
| Transversion |
T>A |
All |
850260 |
4.61 % |
| Transversion |
C>G |
All |
335516 |
1.82 % |
| Transversion |
G>C |
All |
329996 |
1.79 % |
| |
|
|
|
|
| Transition |
A>G |
Passed |
627740 |
17.59 % |
| Transition |
G>A |
Passed |
559001 |
15.66 % |
| Transition |
T>C |
Passed |
626782 |
17.56 % |
| Transition |
C>T |
Passed |
559209 |
15.67 % |
| Transversion |
A>C |
Passed |
150087 |
4.21 % |
| Transversion |
C>A |
Passed |
161187 |
4.52 % |
| Transversion |
T>G |
Passed |
150434 |
4.22 % |
| Transversion |
G>T |
Passed |
160426 |
4.50 % |
| Transversion |
A>T |
Passed |
147356 |
4.13 % |
| Transversion |
T>A |
Passed |
148451 |
4.16 % |
| Transversion |
C>G |
Passed |
139043 |
3.90 % |
| Transversion |
G>C |
Passed |
139207 |
3.90 % |
| |
|
|
|
|
| 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 |
13596879 |
4852193 |
| Passed |
1.98 |
2372732 |
1196191 |
| dbSNPAll |
0 |
0 |
0 |
| dbSNPPassed |
0 |
0 |
0 |