/cemt/variants/A34004_3_lane_gembs
BACK
SAMPLE A34004_3_lane_gembs
Variant counts
| Type |
Total |
Pass |
% |
| SNPs |
1159794204 |
907314219 |
78.23 % |
| Multiallelic |
0 |
0 |
0.00 % |
VCF Filtering Stats
| Type |
#Sites |
% |
#Non-Variant Sites |
% |
#Variant Sites |
% |
| All |
1159794204 |
100% |
1136897719 |
98.03 % |
22896485 |
1.97 % |
| |
|
|
|
|
|
|
| Passed |
910352124 |
78.49 % |
904749073 |
79.58 % |
5603051 |
0.62 % |
| Filtered |
249442080 |
21.51 % |
232148646 |
20.42 % |
17293434 |
1.90 % |
| |
|
|
|
|
|
|
| q20 |
205580519 |
82.42 % |
203832078 |
87.80 % |
1748441 |
10.11 % |
| q20,qd2 |
18902965 |
7.58 % |
3983486 |
1.72 % |
14919479 |
86.27 % |
| q20,mq40 |
17099848 |
6.86 % |
16994528 |
7.32 % |
105320 |
0.61 % |
| mq40 |
4210984 |
1.69 % |
3961829 |
1.71 % |
249155 |
1.44 % |
| q20,qd2,mq40 |
3025541 |
1.21 % |
2869336 |
1.24 % |
156205 |
0.90 % |
| qd2 |
584240 |
0.23 % |
478003 |
0.21 % |
106237 |
0.61 % |
| qd2,mq40 |
37119 |
0.01 % |
29386 |
0.01 % |
7733 |
0.04 % |
| qd2,fs60,mq40 |
389 |
0.00 % |
0 |
0.00 % |
389 |
0.00 % |
| fs60,mq40 |
205 |
0.00 % |
0 |
0.00 % |
205 |
0.00 % |
| qd2,fs60 |
168 |
0.00 % |
0 |
0.00 % |
168 |
0.00 % |
| q20,qd2,fs60,mq40 |
51 |
0.00 % |
0 |
0.00 % |
51 |
0.00 % |
| fs60 |
42 |
0.00 % |
0 |
0.00 % |
42 |
0.00 % |
| q20,qd2,fs60 |
8 |
0.00 % |
0 |
0.00 % |
8 |
0.00 % |
| q20,fs60,mq40 |
1 |
0.00 % |
0 |
0.00 % |
1 |
0.00 % |
| q20,fs60 |
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 |
10106255 |
41.28 % |
| Transition |
G>A |
All |
1011724 |
4.13 % |
| Transition |
T>C |
All |
9648171 |
39.41 % |
| Transition |
C>T |
All |
1037641 |
4.24 % |
| Transversion |
A>C |
All |
206910 |
0.85 % |
| Transversion |
C>A |
All |
483110 |
1.97 % |
| Transversion |
T>G |
All |
220409 |
0.90 % |
| Transversion |
G>T |
All |
467995 |
1.91 % |
| Transversion |
A>T |
All |
431416 |
1.76 % |
| Transversion |
T>A |
All |
446523 |
1.82 % |
| Transversion |
C>G |
All |
214770 |
0.88 % |
| Transversion |
G>C |
All |
206526 |
0.84 % |
| |
|
|
|
|
| Transition |
A>G |
Passed |
670516 |
18.98 % |
| Transition |
G>A |
Passed |
537859 |
15.22 % |
| Transition |
T>C |
Passed |
653239 |
18.49 % |
| Transition |
C>T |
Passed |
542146 |
15.35 % |
| Transversion |
A>C |
Passed |
141196 |
4.00 % |
| Transversion |
C>A |
Passed |
148448 |
4.20 % |
| Transversion |
T>G |
Passed |
142241 |
4.03 % |
| Transversion |
G>T |
Passed |
148925 |
4.22 % |
| Transversion |
A>T |
Passed |
130686 |
3.70 % |
| Transversion |
T>A |
Passed |
131826 |
3.73 % |
| Transversion |
C>G |
Passed |
142558 |
4.04 % |
| Transversion |
G>C |
Passed |
143169 |
4.05 % |
| |
|
|
|
|
| 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 |
8.14 |
21803791 |
2677659 |
| Passed |
2.13 |
2403760 |
1129049 |
| dbSNPAll |
0 |
0 |
0 |
| dbSNPPassed |
0 |
0 |
0 |