/EXTERNAL BLUEPRINT/variants/K006375_15_lane_gembs
BACK
SAMPLE K006375_15_lane_gembs
Variant counts
| Type |
Total |
Pass |
% |
| SNPs |
1150244972 |
1062150561 |
92.34 % |
| Multiallelic |
0 |
0 |
0.00 % |
VCF Filtering Stats
| Type |
#Sites |
% |
#Non-Variant Sites |
% |
#Variant Sites |
% |
| All |
1150244972 |
100% |
1140337852 |
99.14 % |
9907120 |
0.86 % |
| |
|
|
|
|
|
|
| Passed |
1062771324 |
92.40 % |
1059664197 |
92.93 % |
3107127 |
0.29 % |
| Filtered |
87473648 |
7.60 % |
80673655 |
7.07 % |
6799993 |
0.64 % |
| |
|
|
|
|
|
|
| q20 |
55035884 |
62.92 % |
54484857 |
67.54 % |
551027 |
8.10 % |
| q20,mq40 |
12766302 |
14.59 % |
12654803 |
15.69 % |
111499 |
1.64 % |
| q20,qd2 |
9390723 |
10.74 % |
3817734 |
4.73 % |
5572989 |
81.96 % |
| mq40 |
4867545 |
5.56 % |
4660990 |
5.78 % |
206555 |
3.04 % |
| q20,qd2,mq40 |
3012540 |
3.44 % |
2825797 |
3.50 % |
186743 |
2.75 % |
| qd2 |
2351575 |
2.69 % |
2190490 |
2.72 % |
161085 |
2.37 % |
| qd2,mq40 |
47609 |
0.05 % |
38984 |
0.05 % |
8625 |
0.13 % |
| qd2,fs60,mq40 |
624 |
0.00 % |
0 |
0.00 % |
624 |
0.01 % |
| fs60,mq40 |
362 |
0.00 % |
0 |
0.00 % |
362 |
0.01 % |
| qd2,fs60 |
173 |
0.00 % |
0 |
0.00 % |
173 |
0.00 % |
| fs60 |
157 |
0.00 % |
0 |
0.00 % |
157 |
0.00 % |
| q20,qd2,fs60,mq40 |
81 |
0.00 % |
0 |
0.00 % |
81 |
0.00 % |
| q20,qd2,fs60 |
72 |
0.00 % |
0 |
0.00 % |
72 |
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 |
3480412 |
30.11 % |
| Transition |
G>A |
All |
963160 |
8.33 % |
| Transition |
T>C |
All |
3445875 |
29.81 % |
| Transition |
C>T |
All |
981245 |
8.49 % |
| Transversion |
A>C |
All |
225547 |
1.95 % |
| Transversion |
C>A |
All |
502723 |
4.35 % |
| Transversion |
T>G |
All |
227789 |
1.97 % |
| Transversion |
G>T |
All |
497816 |
4.31 % |
| Transversion |
A>T |
All |
415441 |
3.59 % |
| Transversion |
T>A |
All |
408404 |
3.53 % |
| Transversion |
C>G |
All |
205862 |
1.78 % |
| Transversion |
G>C |
All |
205807 |
1.78 % |
| |
|
|
|
|
| Transition |
A>G |
Passed |
625142 |
16.98 % |
| Transition |
G>A |
Passed |
605395 |
16.44 % |
| Transition |
T>C |
Passed |
626623 |
17.02 % |
| Transition |
C>T |
Passed |
611618 |
16.61 % |
| Transversion |
A>C |
Passed |
154819 |
4.20 % |
| Transversion |
C>A |
Passed |
162278 |
4.41 % |
| Transversion |
T>G |
Passed |
155716 |
4.23 % |
| Transversion |
G>T |
Passed |
162413 |
4.41 % |
| Transversion |
A>T |
Passed |
137990 |
3.75 % |
| Transversion |
T>A |
Passed |
137346 |
3.73 % |
| Transversion |
C>G |
Passed |
151635 |
4.12 % |
| Transversion |
G>C |
Passed |
151472 |
4.11 % |
| |
|
|
|
|
| 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 |
3.30 |
8870692 |
2689389 |
| Passed |
2.03 |
2468778 |
1213669 |
| dbSNPAll |
0 |
0 |
0 |
| dbSNPPassed |
0 |
0 |
0 |