/EXTERNAL CREST/variants/K006463_1_lane_gembs
BACK
SAMPLE K006463_1_lane_gembs
Variant counts
| Type |
Total |
Pass |
% |
| SNPs |
1227810394 |
603952554 |
49.19 % |
| Multiallelic |
0 |
0 |
0.00 % |
VCF Filtering Stats
| Type |
#Sites |
% |
#Non-Variant Sites |
% |
#Variant Sites |
% |
| All |
1227810394 |
100% |
1102657443 |
89.81 % |
125152951 |
10.19 % |
| |
|
|
|
|
|
|
| Passed |
624560000 |
50.87 % |
596138998 |
54.06 % |
28421002 |
4.55 % |
| Filtered |
603250394 |
49.13 % |
506518445 |
45.94 % |
96731949 |
15.49 % |
| |
|
|
|
|
|
|
| q20 |
428139942 |
70.97 % |
402564015 |
79.48 % |
25575927 |
26.44 % |
| q20,qd2 |
96488057 |
15.99 % |
32305858 |
6.38 % |
64182199 |
66.35 % |
| q20,mq40 |
45520475 |
7.55 % |
43690455 |
8.63 % |
1830020 |
1.89 % |
| mq40 |
18918043 |
3.14 % |
16818518 |
3.32 % |
2099525 |
2.17 % |
| q20,qd2,mq40 |
7898228 |
1.31 % |
5448200 |
1.08 % |
2450028 |
2.53 % |
| qd2 |
6205687 |
1.03 % |
5626888 |
1.11 % |
578799 |
0.60 % |
| qd2,mq40 |
79252 |
0.01 % |
64511 |
0.01 % |
14741 |
0.02 % |
| fs60 |
391 |
0.00 % |
0 |
0.00 % |
391 |
0.00 % |
| fs60,mq40 |
276 |
0.00 % |
0 |
0.00 % |
276 |
0.00 % |
| q20,qd2,fs60 |
23 |
0.00 % |
0 |
0.00 % |
23 |
0.00 % |
| q20,fs60 |
10 |
0.00 % |
0 |
0.00 % |
10 |
0.00 % |
| qd2,fs60 |
4 |
0.00 % |
0 |
0.00 % |
4 |
0.00 % |
| qd2,fs60,mq40 |
3 |
0.00 % |
0 |
0.00 % |
3 |
0.00 % |
| q20,qd2,fs60,mq40 |
2 |
0.00 % |
0 |
0.00 % |
2 |
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 |
27877659 |
21.92 % |
| Transition |
G>A |
All |
10938135 |
8.60 % |
| Transition |
T>C |
All |
32420048 |
25.49 % |
| Transition |
C>T |
All |
6981810 |
5.49 % |
| Transversion |
A>C |
All |
3151103 |
2.48 % |
| Transversion |
C>A |
All |
7358254 |
5.79 % |
| Transversion |
T>G |
All |
5317307 |
4.18 % |
| Transversion |
G>T |
All |
6871014 |
5.40 % |
| Transversion |
A>T |
All |
9539479 |
7.50 % |
| Transversion |
T>A |
All |
10578327 |
8.32 % |
| Transversion |
C>G |
All |
3622277 |
2.85 % |
| Transversion |
G>C |
All |
2528572 |
1.99 % |
| |
|
|
|
|
| Transition |
A>G |
Passed |
1633853 |
19.85 % |
| Transition |
G>A |
Passed |
757691 |
9.21 % |
| Transition |
T>C |
Passed |
2275009 |
27.64 % |
| Transition |
C>T |
Passed |
420892 |
5.11 % |
| Transversion |
A>C |
Passed |
292256 |
3.55 % |
| Transversion |
C>A |
Passed |
460851 |
5.60 % |
| Transversion |
T>G |
Passed |
553325 |
6.72 % |
| Transversion |
G>T |
Passed |
214726 |
2.61 % |
| Transversion |
A>T |
Passed |
237473 |
2.89 % |
| Transversion |
T>A |
Passed |
645890 |
7.85 % |
| Transversion |
C>G |
Passed |
437724 |
5.32 % |
| Transversion |
G>C |
Passed |
300547 |
3.65 % |
| |
|
|
|
|
| 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 |
1.60 |
78217652 |
48966333 |
| Passed |
1.62 |
5087445 |
3142792 |
| dbSNPAll |
0 |
0 |
0 |
| dbSNPPassed |
0 |
0 |
0 |