/CEMT/variants/A54766_3_lane_gembs
BACK
SAMPLE A54766_3_lane_gembs
Variant counts
| Type |
Total |
Pass |
% |
| SNPs |
1161264486 |
471155267 |
40.57 % |
| Multiallelic |
0 |
0 |
0.00 % |
VCF Filtering Stats
| Type |
#Sites |
% |
#Non-Variant Sites |
% |
#Variant Sites |
% |
| All |
1161264486 |
100% |
1129614731 |
97.27 % |
31649755 |
2.73 % |
| |
|
|
|
|
|
|
| Passed |
476083877 |
41.00 % |
469239823 |
41.54 % |
6844054 |
1.44 % |
| Filtered |
685180609 |
59.00 % |
660374908 |
58.46 % |
24805701 |
5.21 % |
| |
|
|
|
|
|
|
| q20 |
608653150 |
88.83 % |
599960604 |
90.85 % |
8692546 |
35.04 % |
| q20,qd2 |
41259066 |
6.02 % |
26103362 |
3.95 % |
15155704 |
61.10 % |
| qd2 |
16398593 |
2.39 % |
16178088 |
2.45 % |
220505 |
0.89 % |
| q20,mq40 |
13028683 |
1.90 % |
12749363 |
1.93 % |
279320 |
1.13 % |
| q20,qd2,mq40 |
4216768 |
0.62 % |
3964288 |
0.60 % |
252480 |
1.02 % |
| mq40 |
1518912 |
0.22 % |
1352186 |
0.20 % |
166726 |
0.67 % |
| qd2,mq40 |
78393 |
0.01 % |
67017 |
0.01 % |
11376 |
0.05 % |
| q20,qd2,fs60 |
10300 |
0.00 % |
0 |
0.00 % |
10300 |
0.04 % |
| qd2,fs60 |
7764 |
0.00 % |
0 |
0.00 % |
7764 |
0.03 % |
| fs60 |
6486 |
0.00 % |
0 |
0.00 % |
6486 |
0.03 % |
| qd2,fs60,mq40 |
1640 |
0.00 % |
0 |
0.00 % |
1640 |
0.01 % |
| fs60,mq40 |
476 |
0.00 % |
0 |
0.00 % |
476 |
0.00 % |
| q20,qd2,fs60,mq40 |
366 |
0.00 % |
0 |
0.00 % |
366 |
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 |
10279820 |
28.94 % |
| Transition |
G>A |
All |
3186031 |
8.97 % |
| Transition |
T>C |
All |
7513683 |
21.15 % |
| Transition |
C>T |
All |
3213581 |
9.05 % |
| Transversion |
A>C |
All |
899528 |
2.53 % |
| Transversion |
C>A |
All |
1964674 |
5.53 % |
| Transversion |
T>G |
All |
1100380 |
3.10 % |
| Transversion |
G>T |
All |
1818605 |
5.12 % |
| Transversion |
A>T |
All |
1884929 |
5.31 % |
| Transversion |
T>A |
All |
2060399 |
5.80 % |
| Transversion |
C>G |
All |
880557 |
2.48 % |
| Transversion |
G>C |
All |
716583 |
2.02 % |
| |
|
|
|
|
| Transition |
A>G |
Passed |
526209 |
21.16 % |
| Transition |
G>A |
Passed |
350251 |
14.08 % |
| Transition |
T>C |
Passed |
445634 |
17.92 % |
| Transition |
C>T |
Passed |
354899 |
14.27 % |
| Transversion |
A>C |
Passed |
98316 |
3.95 % |
| Transversion |
C>A |
Passed |
110504 |
4.44 % |
| Transversion |
T>G |
Passed |
104372 |
4.20 % |
| Transversion |
G>T |
Passed |
108570 |
4.37 % |
| Transversion |
A>T |
Passed |
99450 |
4.00 % |
| Transversion |
T>A |
Passed |
101731 |
4.09 % |
| Transversion |
C>G |
Passed |
95183 |
3.83 % |
| Transversion |
G>C |
Passed |
91822 |
3.69 % |
| |
|
|
|
|
| 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 |
2.14 |
24193115 |
11325655 |
| Passed |
2.07 |
1676993 |
809948 |
| dbSNPAll |
0 |
0 |
0 |
| dbSNPPassed |
0 |
0 |
0 |