/EXTERNAL BLUEPRINT/variants/K006310_21_lane_gembs
BACK
SAMPLE K006310_21_lane_gembs
Variant counts
| Type |
Total |
Pass |
% |
| SNPs |
1021131323 |
418884644 |
41.02 % |
| Multiallelic |
0 |
0 |
0.00 % |
VCF Filtering Stats
| Type |
#Sites |
% |
#Non-Variant Sites |
% |
#Variant Sites |
% |
| All |
1021131323 |
100% |
1005811366 |
98.50 % |
15319957 |
1.50 % |
| |
|
|
|
|
|
|
| Passed |
420501412 |
41.18 % |
418054890 |
41.56 % |
2446522 |
0.58 % |
| Filtered |
600629911 |
58.82 % |
587756476 |
58.44 % |
12873435 |
3.06 % |
| |
|
|
|
|
|
|
| q20 |
483000958 |
80.42 % |
480748898 |
81.79 % |
2252060 |
17.49 % |
| q20,qd2 |
69909004 |
11.64 % |
59795673 |
10.17 % |
10113331 |
78.56 % |
| qd2 |
20524377 |
3.42 % |
20427815 |
3.48 % |
96562 |
0.75 % |
| q20,mq40 |
16304534 |
2.71 % |
16214305 |
2.76 % |
90229 |
0.70 % |
| mq40 |
7056274 |
1.17 % |
6910747 |
1.18 % |
145527 |
1.13 % |
| q20,qd2,mq40 |
3709061 |
0.62 % |
3563980 |
0.61 % |
145081 |
1.13 % |
| qd2,mq40 |
108655 |
0.02 % |
95058 |
0.02 % |
13597 |
0.11 % |
| qd2,fs60 |
5787 |
0.00 % |
0 |
0.00 % |
5787 |
0.04 % |
| q20,qd2,fs60 |
4745 |
0.00 % |
0 |
0.00 % |
4745 |
0.04 % |
| qd2,fs60,mq40 |
2550 |
0.00 % |
0 |
0.00 % |
2550 |
0.02 % |
| fs60 |
2065 |
0.00 % |
0 |
0.00 % |
2065 |
0.02 % |
| q20,qd2,fs60,mq40 |
1175 |
0.00 % |
0 |
0.00 % |
1175 |
0.01 % |
| fs60,mq40 |
722 |
0.00 % |
0 |
0.00 % |
722 |
0.01 % |
| q20,fs60 |
4 |
0.00 % |
0 |
0.00 % |
4 |
0.00 % |
| q20,fs60,mq40 |
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 |
2869324 |
10.02 % |
| Transition |
G>A |
All |
10452688 |
36.52 % |
| Transition |
T>C |
All |
2415672 |
8.44 % |
| Transition |
C>T |
All |
10304142 |
36.00 % |
| Transversion |
A>C |
All |
216824 |
0.76 % |
| Transversion |
C>A |
All |
489557 |
1.71 % |
| Transversion |
T>G |
All |
258819 |
0.90 % |
| Transversion |
G>T |
All |
463026 |
1.62 % |
| Transversion |
A>T |
All |
365602 |
1.28 % |
| Transversion |
T>A |
All |
397639 |
1.39 % |
| Transversion |
C>G |
All |
205707 |
0.72 % |
| Transversion |
G>C |
All |
183463 |
0.64 % |
| |
|
|
|
|
| Transition |
A>G |
Passed |
236716 |
19.83 % |
| Transition |
G>A |
Passed |
206987 |
17.34 % |
| Transition |
T>C |
Passed |
234848 |
19.67 % |
| Transition |
C>T |
Passed |
206481 |
17.30 % |
| Transversion |
A>C |
Passed |
41175 |
3.45 % |
| Transversion |
C>A |
Passed |
35755 |
3.00 % |
| Transversion |
T>G |
Passed |
40632 |
3.40 % |
| Transversion |
G>T |
Passed |
35912 |
3.01 % |
| Transversion |
A>T |
Passed |
21497 |
1.80 % |
| Transversion |
T>A |
Passed |
20909 |
1.75 % |
| Transversion |
C>G |
Passed |
56361 |
4.72 % |
| Transversion |
G>C |
Passed |
56528 |
4.74 % |
| |
|
|
|
|
| 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 |
10.09 |
26041826 |
2580637 |
| Passed |
2.87 |
885032 |
308769 |
| dbSNPAll |
0 |
0 |
0 |
| dbSNPPassed |
0 |
0 |
0 |