/cemt/variants/A36004_3_lane_gembs
BACK
SAMPLE A36004_3_lane_gembs
Variant counts
| Type |
Total |
Pass |
% |
| SNPs |
1162764222 |
678042500 |
58.31 % |
| Multiallelic |
0 |
0 |
0.00 % |
VCF Filtering Stats
| Type |
#Sites |
% |
#Non-Variant Sites |
% |
#Variant Sites |
% |
| All |
1162764222 |
100% |
1143638651 |
98.36 % |
19125571 |
1.64 % |
| |
|
|
|
|
|
|
| Passed |
680849571 |
58.55 % |
675937721 |
59.10 % |
4911850 |
0.72 % |
| Filtered |
481914651 |
41.45 % |
467700930 |
40.90 % |
14213721 |
2.09 % |
| |
|
|
|
|
|
|
| q20 |
425257607 |
88.24 % |
421442526 |
90.11 % |
3815081 |
26.84 % |
| q20,qd2 |
25033868 |
5.19 % |
15451129 |
3.30 % |
9582739 |
67.42 % |
| qd2 |
15401192 |
3.20 % |
15157815 |
3.24 % |
243377 |
1.71 % |
| q20,mq40 |
10964115 |
2.28 % |
10775849 |
2.30 % |
188266 |
1.32 % |
| q20,qd2,mq40 |
3345008 |
0.69 % |
3141575 |
0.67 % |
203433 |
1.43 % |
| mq40 |
1825077 |
0.38 % |
1673415 |
0.36 % |
151662 |
1.07 % |
| qd2,mq40 |
69100 |
0.01 % |
58621 |
0.01 % |
10479 |
0.07 % |
| q20,qd2,fs60 |
6385 |
0.00 % |
0 |
0.00 % |
6385 |
0.04 % |
| qd2,fs60 |
4874 |
0.00 % |
0 |
0.00 % |
4874 |
0.03 % |
| fs60 |
4793 |
0.00 % |
0 |
0.00 % |
4793 |
0.03 % |
| qd2,fs60,mq40 |
1851 |
0.00 % |
0 |
0.00 % |
1851 |
0.01 % |
| fs60,mq40 |
449 |
0.00 % |
0 |
0.00 % |
449 |
0.00 % |
| q20,qd2,fs60,mq40 |
318 |
0.00 % |
0 |
0.00 % |
318 |
0.00 % |
| q20,fs60 |
14 |
0.00 % |
0 |
0.00 % |
14 |
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 |
5929366 |
27.28 % |
| Transition |
G>A |
All |
1924662 |
8.85 % |
| Transition |
T>C |
All |
5779942 |
26.59 % |
| Transition |
C>T |
All |
1912535 |
8.80 % |
| Transversion |
A>C |
All |
450796 |
2.07 % |
| Transversion |
C>A |
All |
1079165 |
4.97 % |
| Transversion |
T>G |
All |
459792 |
2.12 % |
| Transversion |
G>T |
All |
1078309 |
4.96 % |
| Transversion |
A>T |
All |
1201652 |
5.53 % |
| Transversion |
T>A |
All |
1201587 |
5.53 % |
| Transversion |
C>G |
All |
363303 |
1.67 % |
| Transversion |
G>C |
All |
354261 |
1.63 % |
| |
|
|
|
|
| Transition |
A>G |
Passed |
535982 |
18.14 % |
| Transition |
G>A |
Passed |
450434 |
15.25 % |
| Transition |
T>C |
Passed |
536045 |
18.15 % |
| Transition |
C>T |
Passed |
453310 |
15.35 % |
| Transversion |
A>C |
Passed |
124690 |
4.22 % |
| Transversion |
C>A |
Passed |
130883 |
4.43 % |
| Transversion |
T>G |
Passed |
124843 |
4.23 % |
| Transversion |
G>T |
Passed |
129700 |
4.39 % |
| Transversion |
A>T |
Passed |
120125 |
4.07 % |
| Transversion |
T>A |
Passed |
121276 |
4.11 % |
| Transversion |
C>G |
Passed |
113175 |
3.83 % |
| Transversion |
G>C |
Passed |
113479 |
3.84 % |
| |
|
|
|
|
| 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 |
2.51 |
15546505 |
6188865 |
| Passed |
2.02 |
1975771 |
978171 |
| dbSNPAll |
0 |
0 |
0 |
| dbSNPPassed |
0 |
0 |
0 |