/cemt/variants/A54775_3_lane_gembs
BACK
SAMPLE A54775_3_lane_gembs
Variant counts
| Type |
Total |
Pass |
% |
| SNPs |
1159533392 |
636065908 |
54.86 % |
| Multiallelic |
0 |
0 |
0.00 % |
VCF Filtering Stats
| Type |
#Sites |
% |
#Non-Variant Sites |
% |
#Variant Sites |
% |
| All |
1159533392 |
100% |
1138080019 |
98.15 % |
21453373 |
1.85 % |
| |
|
|
|
|
|
|
| Passed |
639421952 |
55.14 % |
633881896 |
55.70 % |
5540056 |
0.87 % |
| Filtered |
520111440 |
44.86 % |
504198123 |
44.30 % |
15913317 |
2.49 % |
| |
|
|
|
|
|
|
| q20 |
461326398 |
88.70 % |
456823239 |
90.60 % |
4503159 |
28.30 % |
| q20,qd2 |
25747265 |
4.95 % |
15160701 |
3.01 % |
10586564 |
66.53 % |
| qd2 |
17159687 |
3.30 % |
16908720 |
3.35 % |
250967 |
1.58 % |
| q20,mq40 |
10757105 |
2.07 % |
10574843 |
2.10 % |
182262 |
1.15 % |
| q20,qd2,mq40 |
3292891 |
0.63 % |
3088526 |
0.61 % |
204365 |
1.28 % |
| mq40 |
1740237 |
0.33 % |
1581786 |
0.31 % |
158451 |
1.00 % |
| qd2,mq40 |
71975 |
0.01 % |
60308 |
0.01 % |
11667 |
0.07 % |
| q20,qd2,fs60 |
5819 |
0.00 % |
0 |
0.00 % |
5819 |
0.04 % |
| qd2,fs60 |
4285 |
0.00 % |
0 |
0.00 % |
4285 |
0.03 % |
| fs60 |
3282 |
0.00 % |
0 |
0.00 % |
3282 |
0.02 % |
| qd2,fs60,mq40 |
1699 |
0.00 % |
0 |
0.00 % |
1699 |
0.01 % |
| fs60,mq40 |
504 |
0.00 % |
0 |
0.00 % |
504 |
0.00 % |
| q20,qd2,fs60,mq40 |
281 |
0.00 % |
0 |
0.00 % |
281 |
0.00 % |
| q20,fs60 |
10 |
0.00 % |
0 |
0.00 % |
10 |
0.00 % |
| q20,fs60,mq40 |
2 |
0.00 % |
0 |
0.00 % |
2 |
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 |
7274191 |
29.78 % |
| Transition |
G>A |
All |
2301887 |
9.42 % |
| Transition |
T>C |
All |
5947942 |
24.35 % |
| Transition |
C>T |
All |
2353252 |
9.63 % |
| Transversion |
A>C |
All |
423685 |
1.73 % |
| Transversion |
C>A |
All |
1205006 |
4.93 % |
| Transversion |
T>G |
All |
491104 |
2.01 % |
| Transversion |
G>T |
All |
1159301 |
4.75 % |
| Transversion |
A>T |
All |
1216849 |
4.98 % |
| Transversion |
T>A |
All |
1265569 |
5.18 % |
| Transversion |
C>G |
All |
425992 |
1.74 % |
| Transversion |
G>C |
All |
361023 |
1.48 % |
| |
|
|
|
|
| Transition |
A>G |
Passed |
563926 |
19.22 % |
| Transition |
G>A |
Passed |
444789 |
15.16 % |
| Transition |
T>C |
Passed |
522465 |
17.81 % |
| Transition |
C>T |
Passed |
448741 |
15.30 % |
| Transversion |
A>C |
Passed |
119554 |
4.08 % |
| Transversion |
C>A |
Passed |
129565 |
4.42 % |
| Transversion |
T>G |
Passed |
121792 |
4.15 % |
| Transversion |
G>T |
Passed |
128999 |
4.40 % |
| Transversion |
A>T |
Passed |
115923 |
3.95 % |
| Transversion |
T>A |
Passed |
116561 |
3.97 % |
| Transversion |
C>G |
Passed |
111024 |
3.78 % |
| Transversion |
G>C |
Passed |
110479 |
3.77 % |
| |
|
|
|
|
| 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 |
2.73 |
17877272 |
6548529 |
| Passed |
2.08 |
1979921 |
953897 |
| dbSNPAll |
0 |
0 |
0 |
| dbSNPPassed |
0 |
0 |
0 |