/cemt/variants/A83591_2_lane_gembs
BACK
SAMPLE A83591_2_lane_gembs
Variant counts
| Type |
Total |
Pass |
% |
| SNPs |
1169598228 |
841844502 |
71.98 % |
| Multiallelic |
0 |
0 |
0.00 % |
VCF Filtering Stats
| Type |
#Sites |
% |
#Non-Variant Sites |
% |
#Variant Sites |
% |
| All |
1169598228 |
100% |
1149820990 |
98.31 % |
19777238 |
1.69 % |
| |
|
|
|
|
|
|
| Passed |
846043336 |
72.34 % |
839234833 |
72.99 % |
6808503 |
0.80 % |
| Filtered |
323554892 |
27.66 % |
310586157 |
27.01 % |
12968735 |
1.53 % |
| |
|
|
|
|
|
|
| q20 |
291192412 |
90.00 % |
289335482 |
93.16 % |
1856930 |
14.32 % |
| q20,qd2 |
15611308 |
4.82 % |
5229249 |
1.68 % |
10382059 |
80.05 % |
| q20,mq40 |
10069475 |
3.11 % |
9960928 |
3.21 % |
108547 |
0.84 % |
| q20,qd2,mq40 |
2554854 |
0.79 % |
2415346 |
0.78 % |
139508 |
1.08 % |
| mq40 |
2096362 |
0.65 % |
1870377 |
0.60 % |
225985 |
1.74 % |
| qd2 |
1971103 |
0.61 % |
1728986 |
0.56 % |
242117 |
1.87 % |
| qd2,mq40 |
55846 |
0.02 % |
45789 |
0.01 % |
10057 |
0.08 % |
| qd2,fs60,mq40 |
1251 |
0.00 % |
0 |
0.00 % |
1251 |
0.01 % |
| qd2,fs60 |
885 |
0.00 % |
0 |
0.00 % |
885 |
0.01 % |
| fs60 |
564 |
0.00 % |
0 |
0.00 % |
564 |
0.00 % |
| fs60,mq40 |
358 |
0.00 % |
0 |
0.00 % |
358 |
0.00 % |
| q20,qd2,fs60 |
353 |
0.00 % |
0 |
0.00 % |
353 |
0.00 % |
| q20,qd2,fs60,mq40 |
121 |
0.00 % |
0 |
0.00 % |
121 |
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 |
8075502 |
37.40 % |
| Transition |
G>A |
All |
936797 |
4.34 % |
| Transition |
T>C |
All |
8112774 |
37.57 % |
| Transition |
C>T |
All |
942460 |
4.36 % |
| Transversion |
A>C |
All |
432103 |
2.00 % |
| Transversion |
C>A |
All |
556305 |
2.58 % |
| Transversion |
T>G |
All |
430821 |
2.00 % |
| Transversion |
G>T |
All |
548775 |
2.54 % |
| Transversion |
A>T |
All |
385981 |
1.79 % |
| Transversion |
T>A |
All |
386814 |
1.79 % |
| Transversion |
C>G |
All |
391760 |
1.81 % |
| Transversion |
G>C |
All |
394126 |
1.83 % |
| |
|
|
|
|
| Transition |
A>G |
Passed |
711959 |
19.62 % |
| Transition |
G>A |
Passed |
521060 |
14.36 % |
| Transition |
T>C |
Passed |
696651 |
19.20 % |
| Transition |
C>T |
Passed |
521998 |
14.38 % |
| Transversion |
A>C |
Passed |
153582 |
4.23 % |
| Transversion |
C>A |
Passed |
157009 |
4.33 % |
| Transversion |
T>G |
Passed |
153544 |
4.23 % |
| Transversion |
G>T |
Passed |
151583 |
4.18 % |
| Transversion |
A>T |
Passed |
134431 |
3.70 % |
| Transversion |
T>A |
Passed |
135491 |
3.73 % |
| Transversion |
C>G |
Passed |
145796 |
4.02 % |
| Transversion |
G>C |
Passed |
146196 |
4.03 % |
| |
|
|
|
|
| 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 |
5.12 |
18067533 |
3526685 |
| Passed |
2.08 |
2451668 |
1177632 |
| dbSNPAll |
0 |
0 |
0 |
| dbSNPPassed |
0 |
0 |
0 |