/cemt/variants/A34407_3_lane_gembs
BACK
SAMPLE A34407_3_lane_gembs
Variant counts
| Type |
Total |
Pass |
% |
| SNPs |
1155128774 |
584615768 |
50.61 % |
| Multiallelic |
0 |
0 |
0.00 % |
VCF Filtering Stats
| Type |
#Sites |
% |
#Non-Variant Sites |
% |
#Variant Sites |
% |
| All |
1155128774 |
100% |
1132251656 |
98.02 % |
22877118 |
1.98 % |
| |
|
|
|
|
|
|
| Passed |
587831128 |
50.89 % |
581535819 |
51.36 % |
6295309 |
1.07 % |
| Filtered |
567297646 |
49.11 % |
550715837 |
48.64 % |
16581809 |
2.82 % |
| |
|
|
|
|
|
|
| q20 |
503957403 |
88.83 % |
499277395 |
90.66 % |
4680008 |
28.22 % |
| q20,qd2 |
33126513 |
5.84 % |
22286725 |
4.05 % |
10839788 |
65.37 % |
| qd2 |
13816233 |
2.44 % |
13360517 |
2.43 % |
455716 |
2.75 % |
| q20,mq40 |
11138613 |
1.96 % |
10933269 |
1.99 % |
205344 |
1.24 % |
| q20,qd2,mq40 |
3531159 |
0.62 % |
3309659 |
0.60 % |
221500 |
1.34 % |
| mq40 |
1645468 |
0.29 % |
1494779 |
0.27 % |
150689 |
0.91 % |
| qd2,mq40 |
63265 |
0.01 % |
53493 |
0.01 % |
9772 |
0.06 % |
| q20,qd2,fs60 |
7958 |
0.00 % |
0 |
0.00 % |
7958 |
0.05 % |
| fs60 |
4414 |
0.00 % |
0 |
0.00 % |
4414 |
0.03 % |
| qd2,fs60 |
4236 |
0.00 % |
0 |
0.00 % |
4236 |
0.03 % |
| qd2,fs60,mq40 |
1748 |
0.00 % |
0 |
0.00 % |
1748 |
0.01 % |
| fs60,mq40 |
334 |
0.00 % |
0 |
0.00 % |
334 |
0.00 % |
| q20,qd2,fs60,mq40 |
284 |
0.00 % |
0 |
0.00 % |
284 |
0.00 % |
| q20,fs60 |
17 |
0.00 % |
0 |
0.00 % |
17 |
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 |
5777947 |
22.65 % |
| Transition |
G>A |
All |
3021787 |
11.84 % |
| Transition |
T>C |
All |
5645471 |
22.13 % |
| Transition |
C>T |
All |
2986716 |
11.71 % |
| Transversion |
A>C |
All |
525472 |
2.06 % |
| Transversion |
C>A |
All |
1434570 |
5.62 % |
| Transversion |
T>G |
All |
533914 |
2.09 % |
| Transversion |
G>T |
All |
1428341 |
5.60 % |
| Transversion |
A>T |
All |
1653813 |
6.48 % |
| Transversion |
T>A |
All |
1664173 |
6.52 % |
| Transversion |
C>G |
All |
423937 |
1.66 % |
| Transversion |
G>C |
All |
416392 |
1.63 % |
| |
|
|
|
|
| Transition |
A>G |
Passed |
576665 |
17.25 % |
| Transition |
G>A |
Passed |
528727 |
15.81 % |
| Transition |
T>C |
Passed |
578673 |
17.31 % |
| Transition |
C>T |
Passed |
531131 |
15.88 % |
| Transversion |
A>C |
Passed |
136879 |
4.09 % |
| Transversion |
C>A |
Passed |
154285 |
4.61 % |
| Transversion |
T>G |
Passed |
137217 |
4.10 % |
| Transversion |
G>T |
Passed |
153375 |
4.59 % |
| Transversion |
A>T |
Passed |
138616 |
4.15 % |
| Transversion |
T>A |
Passed |
139735 |
4.18 % |
| Transversion |
C>G |
Passed |
134090 |
4.01 % |
| Transversion |
G>C |
Passed |
134538 |
4.02 % |
| |
|
|
|
|
| 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 |
2.16 |
17431921 |
8080612 |
| Passed |
1.96 |
2215196 |
1128735 |
| dbSNPAll |
0 |
0 |
0 |
| dbSNPPassed |
0 |
0 |
0 |