/cemt/variants/A83590_2_lane_gembs
BACK
SAMPLE A83590_2_lane_gembs
Variant counts
| Type |
Total |
Pass |
% |
| SNPs |
1165815773 |
619578379 |
53.15 % |
| Multiallelic |
0 |
0 |
0.00 % |
VCF Filtering Stats
| Type |
#Sites |
% |
#Non-Variant Sites |
% |
#Variant Sites |
% |
| All |
1165815773 |
100% |
1146189817 |
98.32 % |
19625956 |
1.68 % |
| |
|
|
|
|
|
|
| Passed |
625218014 |
53.63 % |
617404180 |
53.87 % |
7813834 |
1.25 % |
| Filtered |
540597759 |
46.37 % |
528785637 |
46.13 % |
11812122 |
1.89 % |
| |
|
|
|
|
|
|
| q20 |
499739952 |
92.44 % |
497098703 |
94.01 % |
2641249 |
22.36 % |
| q20,qd2 |
18069599 |
3.34 % |
9495640 |
1.80 % |
8573959 |
72.59 % |
| q20,mq40 |
9544577 |
1.77 % |
9450945 |
1.79 % |
93632 |
0.79 % |
| qd2 |
8838407 |
1.63 % |
8642627 |
1.63 % |
195780 |
1.66 % |
| q20,qd2,mq40 |
2613853 |
0.48 % |
2504179 |
0.47 % |
109674 |
0.93 % |
| mq40 |
1720968 |
0.32 % |
1544495 |
0.29 % |
176473 |
1.49 % |
| qd2,mq40 |
58493 |
0.01 % |
49048 |
0.01 % |
9445 |
0.08 % |
| qd2,fs60 |
3472 |
0.00 % |
0 |
0.00 % |
3472 |
0.03 % |
| fs60 |
3321 |
0.00 % |
0 |
0.00 % |
3321 |
0.03 % |
| q20,qd2,fs60 |
2461 |
0.00 % |
0 |
0.00 % |
2461 |
0.02 % |
| qd2,fs60,mq40 |
1919 |
0.00 % |
0 |
0.00 % |
1919 |
0.02 % |
| fs60,mq40 |
434 |
0.00 % |
0 |
0.00 % |
434 |
0.00 % |
| q20,qd2,fs60,mq40 |
295 |
0.00 % |
0 |
0.00 % |
295 |
0.00 % |
| q20,fs60 |
5 |
0.00 % |
0 |
0.00 % |
5 |
0.00 % |
| q20,fs60,mq40 |
3 |
0.00 % |
0 |
0.00 % |
3 |
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 |
7548416 |
34.63 % |
| Transition |
G>A |
All |
1212689 |
5.56 % |
| Transition |
T>C |
All |
7547004 |
34.62 % |
| Transition |
C>T |
All |
1220791 |
5.60 % |
| Transversion |
A>C |
All |
520120 |
2.39 % |
| Transversion |
C>A |
All |
707155 |
3.24 % |
| Transversion |
T>G |
All |
519558 |
2.38 % |
| Transversion |
G>T |
All |
698543 |
3.20 % |
| Transversion |
A>T |
All |
455397 |
2.09 % |
| Transversion |
T>A |
All |
457327 |
2.10 % |
| Transversion |
C>G |
All |
454134 |
2.08 % |
| Transversion |
G>C |
All |
455336 |
2.09 % |
| |
|
|
|
|
| Transition |
A>G |
Passed |
572054 |
19.47 % |
| Transition |
G>A |
Passed |
420337 |
14.31 % |
| Transition |
T>C |
Passed |
557061 |
18.96 % |
| Transition |
C>T |
Passed |
421899 |
14.36 % |
| Transversion |
A>C |
Passed |
124740 |
4.25 % |
| Transversion |
C>A |
Passed |
128276 |
4.37 % |
| Transversion |
T>G |
Passed |
125099 |
4.26 % |
| Transversion |
G>T |
Passed |
124777 |
4.25 % |
| Transversion |
A>T |
Passed |
111638 |
3.80 % |
| Transversion |
T>A |
Passed |
112035 |
3.81 % |
| Transversion |
C>G |
Passed |
119985 |
4.08 % |
| Transversion |
G>C |
Passed |
120255 |
4.09 % |
| |
|
|
|
|
| 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 |
4.11 |
17528900 |
4267570 |
| Passed |
2.04 |
1971351 |
966805 |
| dbSNPAll |
0 |
0 |
0 |
| dbSNPPassed |
0 |
0 |
0 |