/cemt/variants/A54770_3_lane_gembs
BACK
SAMPLE A54770_3_lane_gembs
Variant counts
| Type |
Total |
Pass |
% |
| SNPs |
1155997836 |
577517851 |
49.96 % |
| Multiallelic |
0 |
0 |
0.00 % |
VCF Filtering Stats
| Type |
#Sites |
% |
#Non-Variant Sites |
% |
#Variant Sites |
% |
| All |
1155997836 |
100% |
1131536261 |
97.88 % |
24461575 |
2.12 % |
| |
|
|
|
|
|
|
| Passed |
581121781 |
50.27 % |
575519449 |
50.86 % |
5602332 |
0.96 % |
| Filtered |
574876055 |
49.73 % |
556016812 |
49.14 % |
18859243 |
3.25 % |
| |
|
|
|
|
|
|
| q20 |
513257025 |
89.28 % |
507159371 |
91.21 % |
6097654 |
32.33 % |
| q20,qd2 |
34583067 |
6.02 % |
22626588 |
4.07 % |
11956479 |
63.40 % |
| q20,mq40 |
11215983 |
1.95 % |
11012139 |
1.98 % |
203844 |
1.08 % |
| qd2 |
10433571 |
1.81 % |
10219208 |
1.84 % |
214363 |
1.14 % |
| q20,qd2,mq40 |
3689038 |
0.64 % |
3480084 |
0.63 % |
208954 |
1.11 % |
| mq40 |
1617126 |
0.28 % |
1464752 |
0.26 % |
152374 |
0.81 % |
| qd2,mq40 |
64663 |
0.01 % |
54670 |
0.01 % |
9993 |
0.05 % |
| q20,qd2,fs60 |
5776 |
0.00 % |
0 |
0.00 % |
5776 |
0.03 % |
| fs60 |
4084 |
0.00 % |
0 |
0.00 % |
4084 |
0.02 % |
| qd2,fs60 |
3507 |
0.00 % |
0 |
0.00 % |
3507 |
0.02 % |
| qd2,fs60,mq40 |
1558 |
0.00 % |
0 |
0.00 % |
1558 |
0.01 % |
| fs60,mq40 |
400 |
0.00 % |
0 |
0.00 % |
400 |
0.00 % |
| q20,qd2,fs60,mq40 |
248 |
0.00 % |
0 |
0.00 % |
248 |
0.00 % |
| q20,fs60 |
8 |
0.00 % |
0 |
0.00 % |
8 |
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 |
8232083 |
29.43 % |
| Transition |
G>A |
All |
2862228 |
10.23 % |
| Transition |
T>C |
All |
5706211 |
20.40 % |
| Transition |
C>T |
All |
2938862 |
10.51 % |
| Transversion |
A>C |
All |
500148 |
1.79 % |
| Transversion |
C>A |
All |
1687133 |
6.03 % |
| Transversion |
T>G |
All |
622212 |
2.22 % |
| Transversion |
G>T |
All |
1604304 |
5.73 % |
| Transversion |
A>T |
All |
1386352 |
4.96 % |
| Transversion |
T>A |
All |
1468738 |
5.25 % |
| Transversion |
C>G |
All |
542822 |
1.94 % |
| Transversion |
G>C |
All |
423136 |
1.51 % |
| |
|
|
|
|
| Transition |
A>G |
Passed |
545984 |
20.22 % |
| Transition |
G>A |
Passed |
407298 |
15.08 % |
| Transition |
T>C |
Passed |
460711 |
17.06 % |
| Transition |
C>T |
Passed |
410670 |
15.21 % |
| Transversion |
A>C |
Passed |
106119 |
3.93 % |
| Transversion |
C>A |
Passed |
119695 |
4.43 % |
| Transversion |
T>G |
Passed |
109655 |
4.06 % |
| Transversion |
G>T |
Passed |
118221 |
4.38 % |
| Transversion |
A>T |
Passed |
109087 |
4.04 % |
| Transversion |
T>A |
Passed |
110975 |
4.11 % |
| Transversion |
C>G |
Passed |
102041 |
3.78 % |
| Transversion |
G>C |
Passed |
99721 |
3.69 % |
| |
|
|
|
|
| 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 |
2.40 |
19739384 |
8234845 |
| Passed |
2.08 |
1824663 |
875514 |
| dbSNPAll |
0 |
0 |
0 |
| dbSNPPassed |
0 |
0 |
0 |