/CEMT/variants/B04745_2_lane_gembs
BACK
SAMPLE B04745_2_lane_gembs
Variant counts
| Type |
Total |
Pass |
% |
| SNPs |
1169180566 |
813355701 |
69.57 % |
| Multiallelic |
0 |
0 |
0.00 % |
VCF Filtering Stats
| Type |
#Sites |
% |
#Non-Variant Sites |
% |
#Variant Sites |
% |
| All |
1169180566 |
100% |
1149966506 |
98.36 % |
19214060 |
1.64 % |
| |
|
|
|
|
|
|
| Passed |
817655094 |
69.93 % |
810219265 |
70.46 % |
7435829 |
0.91 % |
| Filtered |
351525472 |
30.07 % |
339747241 |
29.54 % |
11778231 |
1.44 % |
| |
|
|
|
|
|
|
| q20 |
315027075 |
89.62 % |
313276780 |
92.21 % |
1750295 |
14.86 % |
| q20,qd2 |
14174819 |
4.03 % |
5011772 |
1.48 % |
9163047 |
77.80 % |
| q20,mq40 |
9553817 |
2.72 % |
9450081 |
2.78 % |
103736 |
0.88 % |
| qd2 |
7952252 |
2.26 % |
7566120 |
2.23 % |
386132 |
3.28 % |
| q20,qd2,mq40 |
2543518 |
0.72 % |
2414271 |
0.71 % |
129247 |
1.10 % |
| mq40 |
2196498 |
0.62 % |
1975751 |
0.58 % |
220747 |
1.87 % |
| qd2,mq40 |
63776 |
0.02 % |
52466 |
0.02 % |
11310 |
0.10 % |
| fs60 |
6223 |
0.00 % |
0 |
0.00 % |
6223 |
0.05 % |
| qd2,fs60 |
3175 |
0.00 % |
0 |
0.00 % |
3175 |
0.03 % |
| q20,qd2,fs60 |
2119 |
0.00 % |
0 |
0.00 % |
2119 |
0.02 % |
| qd2,fs60,mq40 |
1512 |
0.00 % |
0 |
0.00 % |
1512 |
0.01 % |
| fs60,mq40 |
487 |
0.00 % |
0 |
0.00 % |
487 |
0.00 % |
| q20,qd2,fs60,mq40 |
195 |
0.00 % |
0 |
0.00 % |
195 |
0.00 % |
| q20,fs60 |
5 |
0.00 % |
0 |
0.00 % |
5 |
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 |
7655968 |
36.19 % |
| Transition |
G>A |
All |
1128321 |
5.33 % |
| Transition |
T>C |
All |
7626328 |
36.05 % |
| Transition |
C>T |
All |
1140757 |
5.39 % |
| Transversion |
A>C |
All |
313869 |
1.48 % |
| Transversion |
C>A |
All |
766612 |
3.62 % |
| Transversion |
T>G |
All |
318790 |
1.51 % |
| Transversion |
G>T |
All |
630041 |
2.98 % |
| Transversion |
A>T |
All |
447385 |
2.12 % |
| Transversion |
T>A |
All |
519082 |
2.45 % |
| Transversion |
C>G |
All |
306040 |
1.45 % |
| Transversion |
G>C |
All |
299659 |
1.42 % |
| |
|
|
|
|
| Transition |
A>G |
Passed |
840153 |
20.46 % |
| Transition |
G>A |
Passed |
513566 |
12.51 % |
| Transition |
T>C |
Passed |
836450 |
20.37 % |
| Transition |
C>T |
Passed |
513947 |
12.51 % |
| Transversion |
A>C |
Passed |
142323 |
3.47 % |
| Transversion |
C>A |
Passed |
269036 |
6.55 % |
| Transversion |
T>G |
Passed |
144985 |
3.53 % |
| Transversion |
G>T |
Passed |
213565 |
5.20 % |
| Transversion |
A>T |
Passed |
162154 |
3.95 % |
| Transversion |
T>A |
Passed |
186976 |
4.55 % |
| Transversion |
C>G |
Passed |
142403 |
3.47 % |
| Transversion |
G>C |
Passed |
141113 |
3.44 % |
| |
|
|
|
|
| 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 |
4.87 |
17551374 |
3601478 |
| Passed |
1.93 |
2704116 |
1402555 |
| dbSNPAll |
0 |
0 |
0 |
| dbSNPPassed |
0 |
0 |
0 |