/EXTERNAL BLUEPRINT/variants/K006423_1_lane_gembs
BACK
SAMPLE K006423_1_lane_gembs
Variant counts
| Type |
Total |
Pass |
% |
| SNPs |
1156332083 |
1043979850 |
90.28 % |
| Multiallelic |
0 |
0 |
0.00 % |
VCF Filtering Stats
| Type |
#Sites |
% |
#Non-Variant Sites |
% |
#Variant Sites |
% |
| All |
1156332083 |
100% |
1145027114 |
99.02 % |
11304969 |
0.98 % |
| |
|
|
|
|
|
|
| Passed |
1044839833 |
90.36 % |
1041491877 |
90.96 % |
3347956 |
0.32 % |
| Filtered |
111492250 |
9.64 % |
103535237 |
9.04 % |
7957013 |
0.76 % |
| |
|
|
|
|
|
|
| q20 |
78304545 |
70.23 % |
77614868 |
74.96 % |
689677 |
8.67 % |
| q20,mq40 |
12783941 |
11.47 % |
12676586 |
12.24 % |
107355 |
1.35 % |
| q20,qd2 |
11159138 |
10.01 % |
4521348 |
4.37 % |
6637790 |
83.42 % |
| mq40 |
3853080 |
3.46 % |
3658240 |
3.53 % |
194840 |
2.45 % |
| q20,qd2,mq40 |
3076643 |
2.76 % |
2899356 |
2.80 % |
177287 |
2.23 % |
| qd2 |
2267334 |
2.03 % |
2126778 |
2.05 % |
140556 |
1.77 % |
| qd2,mq40 |
46237 |
0.04 % |
38061 |
0.04 % |
8176 |
0.10 % |
| qd2,fs60,mq40 |
627 |
0.00 % |
0 |
0.00 % |
627 |
0.01 % |
| fs60,mq40 |
310 |
0.00 % |
0 |
0.00 % |
310 |
0.00 % |
| qd2,fs60 |
178 |
0.00 % |
0 |
0.00 % |
178 |
0.00 % |
| fs60 |
128 |
0.00 % |
0 |
0.00 % |
128 |
0.00 % |
| q20,qd2,fs60,mq40 |
64 |
0.00 % |
0 |
0.00 % |
64 |
0.00 % |
| q20,qd2,fs60 |
24 |
0.00 % |
0 |
0.00 % |
24 |
0.00 % |
| q20,fs60,mq40 |
1 |
0.00 % |
0 |
0.00 % |
1 |
0.00 % |
| q20,fs60 |
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 |
4071099 |
31.39 % |
| Transition |
G>A |
All |
998177 |
7.70 % |
| Transition |
T>C |
All |
4033328 |
31.10 % |
| Transition |
C>T |
All |
1016188 |
7.84 % |
| Transversion |
A>C |
All |
218593 |
1.69 % |
| Transversion |
C>A |
All |
572959 |
4.42 % |
| Transversion |
T>G |
All |
219763 |
1.69 % |
| Transversion |
G>T |
All |
570116 |
4.40 % |
| Transversion |
A>T |
All |
434605 |
3.35 % |
| Transversion |
T>A |
All |
424067 |
3.27 % |
| Transversion |
C>G |
All |
204985 |
1.58 % |
| Transversion |
G>C |
All |
205199 |
1.58 % |
| |
|
|
|
|
| Transition |
A>G |
Passed |
624368 |
16.99 % |
| Transition |
G>A |
Passed |
606178 |
16.49 % |
| Transition |
T>C |
Passed |
626261 |
17.04 % |
| Transition |
C>T |
Passed |
611444 |
16.64 % |
| Transversion |
A>C |
Passed |
152968 |
4.16 % |
| Transversion |
C>A |
Passed |
160850 |
4.38 % |
| Transversion |
T>G |
Passed |
153163 |
4.17 % |
| Transversion |
G>T |
Passed |
162149 |
4.41 % |
| Transversion |
A>T |
Passed |
137234 |
3.73 % |
| Transversion |
T>A |
Passed |
137141 |
3.73 % |
| Transversion |
C>G |
Passed |
151258 |
4.12 % |
| Transversion |
G>C |
Passed |
152016 |
4.14 % |
| |
|
|
|
|
| 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 |
3.55 |
10118792 |
2850287 |
| Passed |
2.05 |
2468251 |
1206779 |
| dbSNPAll |
0 |
0 |
0 |
| dbSNPPassed |
0 |
0 |
0 |