/EXTERNAL BLUEPRINT/variants/K006334_6_lane_gembs
BACK
SAMPLE K006334_6_lane_gembs
Variant counts
| Type |
Total |
Pass |
% |
| SNPs |
1130507367 |
769306771 |
68.05 % |
| Multiallelic |
0 |
0 |
0.00 % |
VCF Filtering Stats
| Type |
#Sites |
% |
#Non-Variant Sites |
% |
#Variant Sites |
% |
| All |
1130507367 |
100% |
1108361588 |
98.04 % |
22145779 |
1.96 % |
| |
|
|
|
|
|
|
| Passed |
770753333 |
68.18 % |
767726003 |
69.27 % |
3027330 |
0.39 % |
| Filtered |
359754034 |
31.82 % |
340635585 |
30.73 % |
19118449 |
2.48 % |
| |
|
|
|
|
|
|
| q20 |
282881079 |
78.63 % |
280824995 |
82.44 % |
2056084 |
10.75 % |
| q20,qd2 |
45165561 |
12.55 % |
28853660 |
8.47 % |
16311901 |
85.32 % |
| q20,mq40 |
13351027 |
3.71 % |
13219545 |
3.88 % |
131482 |
0.69 % |
| mq40 |
9971021 |
2.77 % |
9772678 |
2.87 % |
198343 |
1.04 % |
| qd2 |
5249244 |
1.46 % |
5115977 |
1.50 % |
133267 |
0.70 % |
| q20,qd2,mq40 |
2977199 |
0.83 % |
2723822 |
0.80 % |
253377 |
1.33 % |
| qd2,mq40 |
142684 |
0.04 % |
124908 |
0.04 % |
17776 |
0.09 % |
| q20,qd2,fs60 |
7405 |
0.00 % |
0 |
0.00 % |
7405 |
0.04 % |
| fs60 |
2921 |
0.00 % |
0 |
0.00 % |
2921 |
0.02 % |
| qd2,fs60,mq40 |
2178 |
0.00 % |
0 |
0.00 % |
2178 |
0.01 % |
| qd2,fs60 |
2062 |
0.00 % |
0 |
0.00 % |
2062 |
0.01 % |
| q20,qd2,fs60,mq40 |
827 |
0.00 % |
0 |
0.00 % |
827 |
0.00 % |
| fs60,mq40 |
819 |
0.00 % |
0 |
0.00 % |
819 |
0.00 % |
| q20,fs60,mq40 |
4 |
0.00 % |
0 |
0.00 % |
4 |
0.00 % |
| q20,fs60 |
3 |
0.00 % |
0 |
0.00 % |
3 |
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 |
3413258 |
9.94 % |
| Transition |
G>A |
All |
12467322 |
36.32 % |
| Transition |
T>C |
All |
3191841 |
9.30 % |
| Transition |
C>T |
All |
12321464 |
35.89 % |
| Transversion |
A>C |
All |
257473 |
0.75 % |
| Transversion |
C>A |
All |
586606 |
1.71 % |
| Transversion |
T>G |
All |
271726 |
0.79 % |
| Transversion |
G>T |
All |
580993 |
1.69 % |
| Transversion |
A>T |
All |
413978 |
1.21 % |
| Transversion |
T>A |
All |
415836 |
1.21 % |
| Transversion |
C>G |
All |
207842 |
0.61 % |
| Transversion |
G>C |
All |
201650 |
0.59 % |
| |
|
|
|
|
| Transition |
A>G |
Passed |
438775 |
18.37 % |
| Transition |
G>A |
Passed |
409923 |
17.16 % |
| Transition |
T>C |
Passed |
438728 |
18.37 % |
| Transition |
C>T |
Passed |
410989 |
17.21 % |
| Transversion |
A>C |
Passed |
92177 |
3.86 % |
| Transversion |
C>A |
Passed |
85249 |
3.57 % |
| Transversion |
T>G |
Passed |
92144 |
3.86 % |
| Transversion |
G>T |
Passed |
85231 |
3.57 % |
| Transversion |
A>T |
Passed |
62255 |
2.61 % |
| Transversion |
T>A |
Passed |
61974 |
2.59 % |
| Transversion |
C>G |
Passed |
105214 |
4.41 % |
| Transversion |
G>C |
Passed |
105764 |
4.43 % |
| |
|
|
|
|
| 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 |
10.69 |
31393885 |
2936104 |
| Passed |
2.46 |
1698415 |
690008 |
| dbSNPAll |
0 |
0 |
0 |
| dbSNPPassed |
0 |
0 |
0 |