/cemt/variants/A83593_2_lane_gembs
BACK
SAMPLE A83593_2_lane_gembs
Variant counts
| Type |
Total |
Pass |
% |
| SNPs |
1170510003 |
882591762 |
75.40 % |
| Multiallelic |
0 |
0 |
0.00 % |
VCF Filtering Stats
| Type |
#Sites |
% |
#Non-Variant Sites |
% |
#Variant Sites |
% |
| All |
1170510003 |
100% |
1150729376 |
98.31 % |
19780627 |
1.69 % |
| |
|
|
|
|
|
|
| Passed |
886464354 |
75.73 % |
879732985 |
76.45 % |
6731369 |
0.76 % |
| Filtered |
284045649 |
24.27 % |
270996391 |
23.55 % |
13049258 |
1.47 % |
| |
|
|
|
|
|
|
| q20 |
252684778 |
88.96 % |
251019836 |
92.63 % |
1664942 |
12.76 % |
| q20,qd2 |
14855342 |
5.23 % |
4194420 |
1.55 % |
10660922 |
81.70 % |
| q20,mq40 |
9933962 |
3.50 % |
9829768 |
3.63 % |
104194 |
0.80 % |
| q20,qd2,mq40 |
2486008 |
0.88 % |
2353939 |
0.87 % |
132069 |
1.01 % |
| mq40 |
2145518 |
0.76 % |
1922632 |
0.71 % |
222886 |
1.71 % |
| qd2 |
1884488 |
0.66 % |
1633308 |
0.60 % |
251180 |
1.92 % |
| qd2,mq40 |
51926 |
0.02 % |
42488 |
0.02 % |
9438 |
0.07 % |
| qd2,fs60,mq40 |
1263 |
0.00 % |
0 |
0.00 % |
1263 |
0.01 % |
| qd2,fs60 |
969 |
0.00 % |
0 |
0.00 % |
969 |
0.01 % |
| fs60 |
658 |
0.00 % |
0 |
0.00 % |
658 |
0.01 % |
| q20,qd2,fs60 |
366 |
0.00 % |
0 |
0.00 % |
366 |
0.00 % |
| fs60,mq40 |
282 |
0.00 % |
0 |
0.00 % |
282 |
0.00 % |
| q20,qd2,fs60,mq40 |
87 |
0.00 % |
0 |
0.00 % |
87 |
0.00 % |
| q20,fs60 |
1 |
0.00 % |
0 |
0.00 % |
1 |
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 |
8082100 |
37.60 % |
| Transition |
G>A |
All |
996373 |
4.64 % |
| Transition |
T>C |
All |
8122854 |
37.79 % |
| Transition |
C>T |
All |
1003940 |
4.67 % |
| Transversion |
A>C |
All |
377843 |
1.76 % |
| Transversion |
C>A |
All |
491323 |
2.29 % |
| Transversion |
T>G |
All |
377655 |
1.76 % |
| Transversion |
G>T |
All |
475549 |
2.21 % |
| Transversion |
A>T |
All |
425282 |
1.98 % |
| Transversion |
T>A |
All |
435475 |
2.03 % |
| Transversion |
C>G |
All |
352915 |
1.64 % |
| Transversion |
G>C |
All |
353973 |
1.65 % |
| |
|
|
|
|
| Transition |
A>G |
Passed |
756747 |
19.46 % |
| Transition |
G>A |
Passed |
559232 |
14.38 % |
| Transition |
T>C |
Passed |
746442 |
19.20 % |
| Transition |
C>T |
Passed |
562384 |
14.47 % |
| Transversion |
A>C |
Passed |
161737 |
4.16 % |
| Transversion |
C>A |
Passed |
172319 |
4.43 % |
| Transversion |
T>G |
Passed |
162001 |
4.17 % |
| Transversion |
G>T |
Passed |
163730 |
4.21 % |
| Transversion |
A>T |
Passed |
145394 |
3.74 % |
| Transversion |
T>A |
Passed |
147940 |
3.81 % |
| Transversion |
C>G |
Passed |
154939 |
3.99 % |
| Transversion |
G>C |
Passed |
154920 |
3.98 % |
| |
|
|
|
|
| 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 |
5.53 |
18205267 |
3290015 |
| Passed |
2.08 |
2624805 |
1262980 |
| dbSNPAll |
0 |
0 |
0 |
| dbSNPPassed |
0 |
0 |
0 |