/EXTERNAL BLUEPRINT/variants/K010451_K010452_K010453_K010454_K010455_K010456_K010457_K010458_K010459_K010460_10_lane_gembs
BACK
SAMPLE K010451_K010452_K010453_K010454_K010455_K010456_K010457_K010458_K010459_K010460_10_lane_gembs
Variant counts
| Type |
Total |
Pass |
% |
| SNPs |
931591747 |
9955687 |
1.07 % |
| Multiallelic |
0 |
0 |
0.00 % |
VCF Filtering Stats
| Type |
#Sites |
% |
#Non-Variant Sites |
% |
#Variant Sites |
% |
| All |
931591747 |
100% |
909577146 |
97.64 % |
22014601 |
2.36 % |
| |
|
|
|
|
|
|
| Passed |
19165374 |
2.06 % |
9291741 |
1.02 % |
9873633 |
51.52 % |
| Filtered |
912426373 |
97.94 % |
900285405 |
98.98 % |
12140968 |
63.35 % |
| |
|
|
|
|
|
|
| q20 |
674968323 |
73.98 % |
666736011 |
74.06 % |
8232312 |
67.81 % |
| q20,qd2 |
128836669 |
14.12 % |
126655570 |
14.07 % |
2181099 |
17.96 % |
| q20,mq40 |
76977457 |
8.44 % |
76224929 |
8.47 % |
752528 |
6.20 % |
| q20,qd2,mq40 |
30564478 |
3.35 % |
30388581 |
3.38 % |
175897 |
1.45 % |
| mq40 |
1069424 |
0.12 % |
271391 |
0.03 % |
798033 |
6.57 % |
| qd2 |
7086 |
0.00 % |
6538 |
0.00 % |
548 |
0.00 % |
| qd2,mq40 |
2908 |
0.00 % |
2385 |
0.00 % |
523 |
0.00 % |
| fs60,mq40 |
11 |
0.00 % |
0 |
0.00 % |
11 |
0.00 % |
| qd2,fs60 |
7 |
0.00 % |
0 |
0.00 % |
7 |
0.00 % |
| 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,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 |
6028969 |
22.60 % |
| Transition |
G>A |
All |
2050939 |
7.69 % |
| Transition |
T>C |
All |
7217331 |
27.05 % |
| Transition |
C>T |
All |
938608 |
3.52 % |
| Transversion |
A>C |
All |
953888 |
3.58 % |
| Transversion |
C>A |
All |
1772906 |
6.65 % |
| Transversion |
T>G |
All |
1171207 |
4.39 % |
| Transversion |
G>T |
All |
1592385 |
5.97 % |
| Transversion |
A>T |
All |
1258090 |
4.72 % |
| Transversion |
T>A |
All |
1717464 |
6.44 % |
| Transversion |
C>G |
All |
923183 |
3.46 % |
| Transversion |
G>C |
All |
1054032 |
3.95 % |
| |
|
|
|
|
| Transition |
A>G |
Passed |
122505 |
18.53 % |
| Transition |
G>A |
Passed |
89100 |
13.48 % |
| Transition |
T>C |
Passed |
184715 |
27.94 % |
| Transition |
C>T |
Passed |
32939 |
4.98 % |
| Transversion |
A>C |
Passed |
26233 |
3.97 % |
| Transversion |
C>A |
Passed |
39077 |
5.91 % |
| Transversion |
T>G |
Passed |
29853 |
4.52 % |
| Transversion |
G>T |
Passed |
20323 |
3.07 % |
| Transversion |
A>T |
Passed |
12391 |
1.87 % |
| Transversion |
T>A |
Passed |
36038 |
5.45 % |
| Transversion |
C>G |
Passed |
28222 |
4.27 % |
| Transversion |
G>C |
Passed |
39752 |
6.01 % |
| |
|
|
|
|
| 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 |
1.55 |
16235847 |
10443155 |
| Passed |
1.85 |
429259 |
231889 |
| dbSNPAll |
0 |
0 |
0 |
| dbSNPPassed |
0 |
0 |
0 |