/EXTERNAL BLUEPRINT/variants/K006352_9_lane_gembs
BACK
SAMPLE K006352_9_lane_gembs
Variant counts
| Type |
Total |
Pass |
% |
| SNPs |
1101339590 |
614132828 |
55.76 % |
| Multiallelic |
0 |
0 |
0.00 % |
VCF Filtering Stats
| Type |
#Sites |
% |
#Non-Variant Sites |
% |
#Variant Sites |
% |
| All |
1101339590 |
100% |
1085588291 |
98.57 % |
15751299 |
1.43 % |
| |
|
|
|
|
|
|
| Passed |
615678783 |
55.90 % |
612877344 |
56.46 % |
2801439 |
0.46 % |
| Filtered |
485660807 |
44.10 % |
472710947 |
43.54 % |
12949860 |
2.10 % |
| |
|
|
|
|
|
|
| q20 |
410436213 |
84.51 % |
408916890 |
86.50 % |
1519323 |
11.73 % |
| q20,qd2 |
49601024 |
10.21 % |
38698289 |
8.19 % |
10902735 |
84.19 % |
| q20,mq40 |
14487968 |
2.98 % |
14385110 |
3.04 % |
102858 |
0.79 % |
| mq40 |
6077637 |
1.25 % |
5928027 |
1.25 % |
149610 |
1.16 % |
| q20,qd2,mq40 |
3277958 |
0.67 % |
3094915 |
0.65 % |
183043 |
1.41 % |
| qd2 |
1702545 |
0.35 % |
1625734 |
0.34 % |
76811 |
0.59 % |
| qd2,mq40 |
71508 |
0.01 % |
61982 |
0.01 % |
9526 |
0.07 % |
| q20,qd2,fs60 |
2036 |
0.00 % |
0 |
0.00 % |
2036 |
0.02 % |
| fs60 |
1225 |
0.00 % |
0 |
0.00 % |
1225 |
0.01 % |
| qd2,fs60,mq40 |
992 |
0.00 % |
0 |
0.00 % |
992 |
0.01 % |
| qd2,fs60 |
796 |
0.00 % |
0 |
0.00 % |
796 |
0.01 % |
| q20,qd2,fs60,mq40 |
463 |
0.00 % |
0 |
0.00 % |
463 |
0.00 % |
| fs60,mq40 |
438 |
0.00 % |
0 |
0.00 % |
438 |
0.00 % |
| q20,fs60,mq40 |
3 |
0.00 % |
0 |
0.00 % |
3 |
0.00 % |
| q20,fs60 |
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 |
2895168 |
15.48 % |
| Transition |
G>A |
All |
5181215 |
27.70 % |
| Transition |
T>C |
All |
2767893 |
14.80 % |
| Transition |
C>T |
All |
5043325 |
26.97 % |
| Transversion |
A>C |
All |
226067 |
1.21 % |
| Transversion |
C>A |
All |
548939 |
2.94 % |
| Transversion |
T>G |
All |
237041 |
1.27 % |
| Transversion |
G>T |
All |
542593 |
2.90 % |
| Transversion |
A>T |
All |
445050 |
2.38 % |
| Transversion |
T>A |
All |
439131 |
2.35 % |
| Transversion |
C>G |
All |
190546 |
1.02 % |
| Transversion |
G>C |
All |
184679 |
0.99 % |
| |
|
|
|
|
| Transition |
A>G |
Passed |
351046 |
18.81 % |
| Transition |
G>A |
Passed |
318753 |
17.08 % |
| Transition |
T>C |
Passed |
349901 |
18.75 % |
| Transition |
C>T |
Passed |
319224 |
17.10 % |
| Transversion |
A>C |
Passed |
71053 |
3.81 % |
| Transversion |
C>A |
Passed |
63785 |
3.42 % |
| Transversion |
T>G |
Passed |
70987 |
3.80 % |
| Transversion |
G>T |
Passed |
64102 |
3.43 % |
| Transversion |
A>T |
Passed |
43767 |
2.34 % |
| Transversion |
T>A |
Passed |
43491 |
2.33 % |
| Transversion |
C>G |
Passed |
85201 |
4.56 % |
| Transversion |
G>C |
Passed |
85243 |
4.57 % |
| |
|
|
|
|
| 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 |
5.65 |
15887601 |
2814046 |
| Passed |
2.54 |
1338924 |
527629 |
| dbSNPAll |
0 |
0 |
0 |
| dbSNPPassed |
0 |
0 |
0 |