/EXTERNAL BLUEPRINT/variants/K006411_12_lane_gembs
BACK
SAMPLE K006411_12_lane_gembs
Variant counts
| Type |
Total |
Pass |
% |
| SNPs |
1157355899 |
1045319934 |
90.32 % |
| Multiallelic |
0 |
0 |
0.00 % |
VCF Filtering Stats
| Type |
#Sites |
% |
#Non-Variant Sites |
% |
#Variant Sites |
% |
| All |
1157355899 |
100% |
1145144686 |
98.94 % |
12211213 |
1.06 % |
| |
|
|
|
|
|
|
| Passed |
1046222930 |
90.40 % |
1042810007 |
91.06 % |
3412923 |
0.33 % |
| Filtered |
111132969 |
9.60 % |
102334679 |
8.94 % |
8798290 |
0.84 % |
| |
|
|
|
|
|
|
| q20 |
78204554 |
70.37 % |
77498894 |
75.73 % |
705660 |
8.02 % |
| q20,mq40 |
12730759 |
11.46 % |
12627517 |
12.34 % |
103242 |
1.17 % |
| q20,qd2 |
11711674 |
10.54 % |
4245948 |
4.15 % |
7465726 |
84.85 % |
| mq40 |
3678622 |
3.31 % |
3486375 |
3.41 % |
192247 |
2.19 % |
| q20,qd2,mq40 |
3075975 |
2.77 % |
2900736 |
2.83 % |
175239 |
1.99 % |
| qd2 |
1685567 |
1.52 % |
1538928 |
1.50 % |
146639 |
1.67 % |
| qd2,mq40 |
44530 |
0.04 % |
36281 |
0.04 % |
8249 |
0.09 % |
| qd2,fs60,mq40 |
598 |
0.00 % |
0 |
0.00 % |
598 |
0.01 % |
| fs60,mq40 |
301 |
0.00 % |
0 |
0.00 % |
301 |
0.00 % |
| qd2,fs60 |
184 |
0.00 % |
0 |
0.00 % |
184 |
0.00 % |
| fs60 |
124 |
0.00 % |
0 |
0.00 % |
124 |
0.00 % |
| q20,qd2,fs60,mq40 |
60 |
0.00 % |
0 |
0.00 % |
60 |
0.00 % |
| q20,qd2,fs60 |
19 |
0.00 % |
0 |
0.00 % |
19 |
0.00 % |
| q20,fs60,mq40 |
2 |
0.00 % |
0 |
0.00 % |
2 |
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 |
4535723 |
32.75 % |
| Transition |
G>A |
All |
940278 |
6.79 % |
| Transition |
T>C |
All |
4502690 |
32.51 % |
| Transition |
C>T |
All |
945046 |
6.82 % |
| Transversion |
A>C |
All |
215646 |
1.56 % |
| Transversion |
C>A |
All |
583337 |
4.21 % |
| Transversion |
T>G |
All |
217731 |
1.57 % |
| Transversion |
G>T |
All |
572155 |
4.13 % |
| Transversion |
A>T |
All |
466351 |
3.37 % |
| Transversion |
T>A |
All |
464277 |
3.35 % |
| Transversion |
C>G |
All |
203968 |
1.47 % |
| Transversion |
G>C |
All |
204268 |
1.47 % |
| |
|
|
|
|
| Transition |
A>G |
Passed |
638955 |
17.33 % |
| Transition |
G>A |
Passed |
599342 |
16.25 % |
| Transition |
T>C |
Passed |
639635 |
17.34 % |
| Transition |
C>T |
Passed |
602551 |
16.34 % |
| Transversion |
A>C |
Passed |
153765 |
4.17 % |
| Transversion |
C>A |
Passed |
159256 |
4.32 % |
| Transversion |
T>G |
Passed |
154115 |
4.18 % |
| Transversion |
G>T |
Passed |
160109 |
4.34 % |
| Transversion |
A>T |
Passed |
136412 |
3.70 % |
| Transversion |
T>A |
Passed |
136893 |
3.71 % |
| Transversion |
C>G |
Passed |
153311 |
4.16 % |
| Transversion |
G>C |
Passed |
153597 |
4.16 % |
| |
|
|
|
|
| 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 |
3.73 |
10923737 |
2927733 |
| Passed |
2.05 |
2480483 |
1207458 |
| dbSNPAll |
0 |
0 |
0 |
| dbSNPPassed |
0 |
0 |
0 |