/EXTERNAL BLUEPRINT/variants/K010402_K010403_K010404_K010405_K010406_K010407_K010408_K010409_K010410_K010411_K010412_11_lane_gembs
BACK
SAMPLE K010402_K010403_K010404_K010405_K010406_K010407_K010408_K010409_K010410_K010411_K010412_11_lane_gembs
Variant counts
| Type |
Total |
Pass |
% |
| SNPs |
930727480 |
10094554 |
1.08 % |
| Multiallelic |
0 |
0 |
0.00 % |
VCF Filtering Stats
| Type |
#Sites |
% |
#Non-Variant Sites |
% |
#Variant Sites |
% |
| All |
930727480 |
100% |
908934258 |
97.66 % |
21793222 |
2.34 % |
| |
|
|
|
|
|
|
| Passed |
19048552 |
2.05 % |
9403549 |
1.03 % |
9645003 |
50.63 % |
| Filtered |
911678928 |
97.95 % |
899530709 |
98.97 % |
12148219 |
63.78 % |
| |
|
|
|
|
|
|
| q20 |
688883228 |
75.56 % |
680374983 |
75.64 % |
8508245 |
70.04 % |
| q20,qd2 |
131065785 |
14.38 % |
128821715 |
14.32 % |
2244070 |
18.47 % |
| q20,mq40 |
64406027 |
7.06 % |
63776460 |
7.09 % |
629567 |
5.18 % |
| q20,qd2,mq40 |
26477179 |
2.90 % |
26333155 |
2.93 % |
144024 |
1.19 % |
| mq40 |
835867 |
0.09 % |
214765 |
0.02 % |
621102 |
5.11 % |
| qd2 |
7915 |
0.00 % |
7332 |
0.00 % |
583 |
0.00 % |
| qd2,mq40 |
2866 |
0.00 % |
2299 |
0.00 % |
567 |
0.00 % |
| fs60,mq40 |
19 |
0.00 % |
0 |
0.00 % |
19 |
0.00 % |
| qd2,fs60 |
18 |
0.00 % |
0 |
0.00 % |
18 |
0.00 % |
| fs60 |
14 |
0.00 % |
0 |
0.00 % |
14 |
0.00 % |
| qd2,fs60,mq40 |
7 |
0.00 % |
0 |
0.00 % |
7 |
0.00 % |
| q20,qd2,fs60,mq40 |
2 |
0.00 % |
0 |
0.00 % |
2 |
0.00 % |
| q20,qd2,fs60 |
1 |
0.00 % |
0 |
0.00 % |
1 |
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 |
5875687 |
22.29 % |
| Transition |
G>A |
All |
2052351 |
7.79 % |
| Transition |
T>C |
All |
7248021 |
27.50 % |
| Transition |
C>T |
All |
930749 |
3.53 % |
| Transversion |
A>C |
All |
975754 |
3.70 % |
| Transversion |
C>A |
All |
1719031 |
6.52 % |
| Transversion |
T>G |
All |
1199910 |
4.55 % |
| Transversion |
G>T |
All |
1536121 |
5.83 % |
| Transversion |
A>T |
All |
1204929 |
4.57 % |
| Transversion |
T>A |
All |
1657397 |
6.29 % |
| Transversion |
C>G |
All |
919218 |
3.49 % |
| Transversion |
G>C |
All |
1039965 |
3.95 % |
| |
|
|
|
|
| Transition |
A>G |
Passed |
126401 |
18.35 % |
| Transition |
G>A |
Passed |
93333 |
13.55 % |
| Transition |
T>C |
Passed |
197466 |
28.67 % |
| Transition |
C>T |
Passed |
33392 |
4.85 % |
| Transversion |
A>C |
Passed |
26617 |
3.86 % |
| Transversion |
C>A |
Passed |
41469 |
6.02 % |
| Transversion |
T>G |
Passed |
30426 |
4.42 % |
| Transversion |
G>T |
Passed |
20444 |
2.97 % |
| Transversion |
A>T |
Passed |
12472 |
1.81 % |
| Transversion |
T>A |
Passed |
37818 |
5.49 % |
| Transversion |
C>G |
Passed |
28764 |
4.18 % |
| Transversion |
G>C |
Passed |
40217 |
5.84 % |
| |
|
|
|
|
| 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 |
1.57 |
16106808 |
10252325 |
| Passed |
1.89 |
450592 |
238227 |
| dbSNPAll |
0 |
0 |
0 |
| dbSNPPassed |
0 |
0 |
0 |