/CEMT/variants/A95341_2_lane_gembs
BACK
SAMPLE A95341_2_lane_gembs
Variant counts
| Type |
Total |
Pass |
% |
| SNPs |
1164966630 |
1081309454 |
92.82 % |
| Multiallelic |
0 |
0 |
0.00 % |
VCF Filtering Stats
| Type |
#Sites |
% |
#Non-Variant Sites |
% |
#Variant Sites |
% |
| All |
1164966630 |
100% |
1155203544 |
99.16 % |
9763086 |
0.84 % |
| |
|
|
|
|
|
|
| Passed |
1082000159 |
92.88 % |
1078402302 |
93.35 % |
3597857 |
0.33 % |
| Filtered |
82966471 |
7.12 % |
76801242 |
6.65 % |
6165229 |
0.57 % |
| |
|
|
|
|
|
|
| q20 |
39407559 |
47.50 % |
38932777 |
50.69 % |
474782 |
7.70 % |
| qd2 |
20834119 |
25.11 % |
20447471 |
26.62 % |
386648 |
6.27 % |
| q20,mq40 |
9321470 |
11.24 % |
9201798 |
11.98 % |
119672 |
1.94 % |
| q20,qd2 |
6595946 |
7.95 % |
1935094 |
2.52 % |
4660852 |
75.60 % |
| mq40 |
4402732 |
5.31 % |
4109437 |
5.35 % |
293295 |
4.76 % |
| q20,qd2,mq40 |
2284981 |
2.75 % |
2092502 |
2.72 % |
192479 |
3.12 % |
| qd2,mq40 |
98898 |
0.12 % |
82163 |
0.11 % |
16735 |
0.27 % |
| fs60 |
8320 |
0.01 % |
0 |
0.00 % |
8320 |
0.13 % |
| qd2,fs60 |
5696 |
0.01 % |
0 |
0.00 % |
5696 |
0.09 % |
| q20,qd2,fs60 |
3706 |
0.00 % |
0 |
0.00 % |
3706 |
0.06 % |
| qd2,fs60,mq40 |
2123 |
0.00 % |
0 |
0.00 % |
2123 |
0.03 % |
| fs60,mq40 |
655 |
0.00 % |
0 |
0.00 % |
655 |
0.01 % |
| q20,qd2,fs60,mq40 |
258 |
0.00 % |
0 |
0.00 % |
258 |
0.00 % |
| q20,fs60 |
7 |
0.00 % |
0 |
0.00 % |
7 |
0.00 % |
| q20,fs60,mq40 |
1 |
0.00 % |
0 |
0.00 % |
1 |
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 |
3624061 |
31.33 % |
| Transition |
G>A |
All |
998608 |
8.63 % |
| Transition |
T>C |
All |
3590540 |
31.04 % |
| Transition |
C>T |
All |
999679 |
8.64 % |
| Transversion |
A>C |
All |
287050 |
2.48 % |
| Transversion |
C>A |
All |
333526 |
2.88 % |
| Transversion |
T>G |
All |
293485 |
2.54 % |
| Transversion |
G>T |
All |
326026 |
2.82 % |
| Transversion |
A>T |
All |
304656 |
2.63 % |
| Transversion |
T>A |
All |
308315 |
2.67 % |
| Transversion |
C>G |
All |
252685 |
2.18 % |
| Transversion |
G>C |
All |
250069 |
2.16 % |
| |
|
|
|
|
| Transition |
A>G |
Passed |
750810 |
17.98 % |
| Transition |
G>A |
Passed |
647354 |
15.51 % |
| Transition |
T>C |
Passed |
760736 |
18.22 % |
| Transition |
C>T |
Passed |
648250 |
15.53 % |
| Transversion |
A>C |
Passed |
180165 |
4.32 % |
| Transversion |
C>A |
Passed |
183539 |
4.40 % |
| Transversion |
T>G |
Passed |
179751 |
4.31 % |
| Transversion |
G>T |
Passed |
175738 |
4.21 % |
| Transversion |
A>T |
Passed |
149686 |
3.59 % |
| Transversion |
T>A |
Passed |
151747 |
3.63 % |
| Transversion |
C>G |
Passed |
172942 |
4.14 % |
| Transversion |
G>C |
Passed |
174040 |
4.17 % |
| |
|
|
|
|
| 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 |
3.91 |
9212888 |
2355812 |
| Passed |
2.05 |
2807150 |
1367608 |
| dbSNPAll |
0 |
0 |
0 |
| dbSNPPassed |
0 |
0 |
0 |