/cemt/variants/A34409_3_lane_gembs
BACK
SAMPLE A34409_3_lane_gembs
Variant counts
| Type |
Total |
Pass |
% |
| SNPs |
1156771937 |
579646332 |
50.11 % |
| Multiallelic |
0 |
0 |
0.00 % |
VCF Filtering Stats
| Type |
#Sites |
% |
#Non-Variant Sites |
% |
#Variant Sites |
% |
| All |
1156771937 |
100% |
1134228895 |
98.05 % |
22543042 |
1.95 % |
| |
|
|
|
|
|
|
| Passed |
583398762 |
50.43 % |
576707345 |
50.85 % |
6691417 |
1.15 % |
| Filtered |
573373175 |
49.57 % |
557521550 |
49.15 % |
15851625 |
2.72 % |
| |
|
|
|
|
|
|
| q20 |
514933605 |
89.81 % |
510612144 |
91.59 % |
4321461 |
27.26 % |
| q20,qd2 |
29387305 |
5.13 % |
18773301 |
3.37 % |
10614004 |
66.96 % |
| qd2 |
13987880 |
2.44 % |
13582481 |
2.44 % |
405399 |
2.56 % |
| q20,mq40 |
10346820 |
1.80 % |
10185670 |
1.83 % |
161150 |
1.02 % |
| q20,qd2,mq40 |
3250448 |
0.57 % |
3074130 |
0.55 % |
176318 |
1.11 % |
| mq40 |
1389429 |
0.24 % |
1243868 |
0.22 % |
145561 |
0.92 % |
| qd2,mq40 |
59870 |
0.01 % |
49956 |
0.01 % |
9914 |
0.06 % |
| q20,qd2,fs60 |
5811 |
0.00 % |
0 |
0.00 % |
5811 |
0.04 % |
| fs60 |
4900 |
0.00 % |
0 |
0.00 % |
4900 |
0.03 % |
| qd2,fs60 |
4848 |
0.00 % |
0 |
0.00 % |
4848 |
0.03 % |
| qd2,fs60,mq40 |
1637 |
0.00 % |
0 |
0.00 % |
1637 |
0.01 % |
| fs60,mq40 |
385 |
0.00 % |
0 |
0.00 % |
385 |
0.00 % |
| q20,qd2,fs60,mq40 |
219 |
0.00 % |
0 |
0.00 % |
219 |
0.00 % |
| q20,fs60 |
18 |
0.00 % |
0 |
0.00 % |
18 |
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 |
6309836 |
25.45 % |
| Transition |
G>A |
All |
2473788 |
9.98 % |
| Transition |
T>C |
All |
6137679 |
24.76 % |
| Transition |
C>T |
All |
2457471 |
9.91 % |
| Transversion |
A>C |
All |
470641 |
1.90 % |
| Transversion |
C>A |
All |
1542117 |
6.22 % |
| Transversion |
T>G |
All |
480585 |
1.94 % |
| Transversion |
G>T |
All |
1538218 |
6.20 % |
| Transversion |
A>T |
All |
1291292 |
5.21 % |
| Transversion |
T>A |
All |
1313015 |
5.30 % |
| Transversion |
C>G |
All |
392860 |
1.58 % |
| Transversion |
G>C |
All |
382550 |
1.54 % |
| |
|
|
|
|
| Transition |
A>G |
Passed |
560435 |
17.41 % |
| Transition |
G>A |
Passed |
497089 |
15.44 % |
| Transition |
T>C |
Passed |
561667 |
17.45 % |
| Transition |
C>T |
Passed |
499598 |
15.52 % |
| Transversion |
A>C |
Passed |
134505 |
4.18 % |
| Transversion |
C>A |
Passed |
149212 |
4.64 % |
| Transversion |
T>G |
Passed |
135391 |
4.21 % |
| Transversion |
G>T |
Passed |
147931 |
4.60 % |
| Transversion |
A>T |
Passed |
133756 |
4.16 % |
| Transversion |
T>A |
Passed |
135207 |
4.20 % |
| Transversion |
C>G |
Passed |
131946 |
4.10 % |
| Transversion |
G>C |
Passed |
132042 |
4.10 % |
| |
|
|
|
|
| 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 |
2.34 |
17378774 |
7411278 |
| Passed |
1.93 |
2118789 |
1099990 |
| dbSNPAll |
0 |
0 |
0 |
| dbSNPPassed |
0 |
0 |
0 |