/EXTERNAL BLUEPRINT/variants/K006380_15_lane_gembs
BACK
SAMPLE K006380_15_lane_gembs
Variant counts
| Type |
Total |
Pass |
% |
| SNPs |
1156330722 |
1064652304 |
92.07 % |
| Multiallelic |
0 |
0 |
0.00 % |
VCF Filtering Stats
| Type |
#Sites |
% |
#Non-Variant Sites |
% |
#Variant Sites |
% |
| All |
1156330722 |
100% |
1146313575 |
99.13 % |
10017147 |
0.87 % |
| |
|
|
|
|
|
|
| Passed |
1065350128 |
92.13 % |
1062143798 |
92.66 % |
3206330 |
0.30 % |
| Filtered |
90980594 |
7.87 % |
84169777 |
7.34 % |
6810817 |
0.64 % |
| |
|
|
|
|
|
|
| q20 |
60607877 |
66.62 % |
60063070 |
71.36 % |
544807 |
8.00 % |
| q20,mq40 |
12229726 |
13.44 % |
12131820 |
14.41 % |
97906 |
1.44 % |
| q20,qd2 |
9139362 |
10.05 % |
3502517 |
4.16 % |
5636845 |
82.76 % |
| mq40 |
4236089 |
4.66 % |
4042460 |
4.80 % |
193629 |
2.84 % |
| q20,qd2,mq40 |
3030146 |
3.33 % |
2857791 |
3.40 % |
172355 |
2.53 % |
| qd2 |
1686155 |
1.85 % |
1530885 |
1.82 % |
155270 |
2.28 % |
| qd2,mq40 |
49809 |
0.05 % |
41234 |
0.05 % |
8575 |
0.13 % |
| qd2,fs60,mq40 |
680 |
0.00 % |
0 |
0.00 % |
680 |
0.01 % |
| fs60,mq40 |
305 |
0.00 % |
0 |
0.00 % |
305 |
0.00 % |
| qd2,fs60 |
167 |
0.00 % |
0 |
0.00 % |
167 |
0.00 % |
| fs60 |
140 |
0.00 % |
0 |
0.00 % |
140 |
0.00 % |
| q20,qd2,fs60,mq40 |
80 |
0.00 % |
0 |
0.00 % |
80 |
0.00 % |
| q20,qd2,fs60 |
51 |
0.00 % |
0 |
0.00 % |
51 |
0.00 % |
| q20,fs60,mq40 |
7 |
0.00 % |
0 |
0.00 % |
7 |
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 |
3600685 |
30.89 % |
| Transition |
G>A |
All |
904831 |
7.76 % |
| Transition |
T>C |
All |
3568420 |
30.61 % |
| Transition |
C>T |
All |
907972 |
7.79 % |
| Transversion |
A>C |
All |
226606 |
1.94 % |
| Transversion |
C>A |
All |
475855 |
4.08 % |
| Transversion |
T>G |
All |
229394 |
1.97 % |
| Transversion |
G>T |
All |
465557 |
3.99 % |
| Transversion |
A>T |
All |
432232 |
3.71 % |
| Transversion |
T>A |
All |
432195 |
3.71 % |
| Transversion |
C>G |
All |
206007 |
1.77 % |
| Transversion |
G>C |
All |
206886 |
1.77 % |
| |
|
|
|
|
| Transition |
A>G |
Passed |
628560 |
16.98 % |
| Transition |
G>A |
Passed |
604916 |
16.34 % |
| Transition |
T>C |
Passed |
630210 |
17.02 % |
| Transition |
C>T |
Passed |
607309 |
16.40 % |
| Transversion |
A>C |
Passed |
158484 |
4.28 % |
| Transversion |
C>A |
Passed |
161597 |
4.36 % |
| Transversion |
T>G |
Passed |
159709 |
4.31 % |
| Transversion |
G>T |
Passed |
161669 |
4.37 % |
| Transversion |
A>T |
Passed |
139190 |
3.76 % |
| Transversion |
T>A |
Passed |
139233 |
3.76 % |
| Transversion |
C>G |
Passed |
155521 |
4.20 % |
| Transversion |
G>C |
Passed |
155876 |
4.21 % |
| |
|
|
|
|
| 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 |
3.36 |
8981908 |
2674732 |
| Passed |
2.01 |
2470995 |
1231279 |
| dbSNPAll |
0 |
0 |
0 |
| dbSNPPassed |
0 |
0 |
0 |