/EXTERNAL BLUEPRINT/variants/K006323_8_lane_gembs
BACK
SAMPLE K006323_8_lane_gembs
Variant counts
| Type |
Total |
Pass |
% |
| SNPs |
1096835892 |
206560857 |
18.83 % |
| Multiallelic |
0 |
0 |
0.00 % |
VCF Filtering Stats
| Type |
#Sites |
% |
#Non-Variant Sites |
% |
#Variant Sites |
% |
| All |
1096835892 |
100% |
1071199369 |
97.66 % |
25636523 |
2.34 % |
| |
|
|
|
|
|
|
| Passed |
214481430 |
19.55 % |
205568478 |
19.19 % |
8912952 |
4.16 % |
| Filtered |
882354462 |
80.45 % |
865630891 |
80.81 % |
16723571 |
7.80 % |
| |
|
|
|
|
|
|
| q20 |
796375985 |
90.26 % |
789748508 |
91.23 % |
6627477 |
39.63 % |
| q20,qd2 |
67080024 |
7.60 % |
57255066 |
6.61 % |
9824958 |
58.75 % |
| q20,mq40 |
12796565 |
1.45 % |
12705906 |
1.47 % |
90659 |
0.54 % |
| q20,qd2,mq40 |
5680189 |
0.64 % |
5618860 |
0.65 % |
61329 |
0.37 % |
| mq40 |
322144 |
0.04 % |
215367 |
0.02 % |
106777 |
0.64 % |
| qd2 |
84937 |
0.01 % |
75394 |
0.01 % |
9543 |
0.06 % |
| qd2,mq40 |
14238 |
0.00 % |
11790 |
0.00 % |
2448 |
0.01 % |
| qd2,fs60,mq40 |
172 |
0.00 % |
0 |
0.00 % |
172 |
0.00 % |
| fs60,mq40 |
74 |
0.00 % |
0 |
0.00 % |
74 |
0.00 % |
| qd2,fs60 |
62 |
0.00 % |
0 |
0.00 % |
62 |
0.00 % |
| q20,qd2,fs60,mq40 |
48 |
0.00 % |
0 |
0.00 % |
48 |
0.00 % |
| fs60 |
18 |
0.00 % |
0 |
0.00 % |
18 |
0.00 % |
| q20,qd2,fs60 |
6 |
0.00 % |
0 |
0.00 % |
6 |
0.00 % |
| q20,fs60 |
0 |
0.00 % |
0 |
0.00 % |
0 |
0.00 % |
| q20,fs60,mq40 |
0 |
0.00 % |
0 |
0.00 % |
0 |
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 |
8431642 |
30.44 % |
| Transition |
G>A |
All |
1205252 |
4.35 % |
| Transition |
T>C |
All |
8479076 |
30.61 % |
| Transition |
C>T |
All |
1209324 |
4.37 % |
| Transversion |
A>C |
All |
433398 |
1.56 % |
| Transversion |
C>A |
All |
1475838 |
5.33 % |
| Transversion |
T>G |
All |
431618 |
1.56 % |
| Transversion |
G>T |
All |
1464048 |
5.29 % |
| Transversion |
A>T |
All |
1962960 |
7.09 % |
| Transversion |
T>A |
All |
1975739 |
7.13 % |
| Transversion |
C>G |
All |
314694 |
1.14 % |
| Transversion |
G>C |
All |
316749 |
1.14 % |
| |
|
|
|
|
| Transition |
A>G |
Passed |
231037 |
19.08 % |
| Transition |
G>A |
Passed |
175778 |
14.52 % |
| Transition |
T>C |
Passed |
229775 |
18.97 % |
| Transition |
C>T |
Passed |
177383 |
14.65 % |
| Transversion |
A>C |
Passed |
49321 |
4.07 % |
| Transversion |
C>A |
Passed |
53441 |
4.41 % |
| Transversion |
T>G |
Passed |
49404 |
4.08 % |
| Transversion |
G>T |
Passed |
52472 |
4.33 % |
| Transversion |
A>T |
Passed |
49951 |
4.12 % |
| Transversion |
T>A |
Passed |
50914 |
4.20 % |
| Transversion |
C>G |
Passed |
45600 |
3.77 % |
| Transversion |
G>C |
Passed |
45906 |
3.79 % |
| |
|
|
|
|
| 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 |
2.31 |
19325294 |
8375044 |
| Passed |
2.05 |
813973 |
397009 |
| dbSNPAll |
0 |
0 |
0 |
| dbSNPPassed |
0 |
0 |
0 |