/EXTERNAL BLUEPRINT/variants/K006285_14_lane_gembs
BACK
SAMPLE K006285_14_lane_gembs
Variant counts
| Type |
Total |
Pass |
% |
| SNPs |
1128598904 |
643612618 |
57.03 % |
| Multiallelic |
0 |
0 |
0.00 % |
VCF Filtering Stats
| Type |
#Sites |
% |
#Non-Variant Sites |
% |
#Variant Sites |
% |
| All |
1128598904 |
100% |
1116956040 |
98.97 % |
11642864 |
1.03 % |
| |
|
|
|
|
|
|
| Passed |
646016884 |
57.24 % |
642147645 |
57.49 % |
3869239 |
0.60 % |
| Filtered |
482582020 |
42.76 % |
474808395 |
42.51 % |
7773625 |
1.20 % |
| |
|
|
|
|
|
|
| q20 |
434722517 |
90.08 % |
433016905 |
91.20 % |
1705612 |
21.94 % |
| q20,qd2 |
23962840 |
4.97 % |
18417423 |
3.88 % |
5545417 |
71.34 % |
| q20,mq40 |
14145198 |
2.93 % |
14052344 |
2.96 % |
92854 |
1.19 % |
| mq40 |
5248567 |
1.09 % |
5077630 |
1.07 % |
170937 |
2.20 % |
| q20,qd2,mq40 |
2775139 |
0.58 % |
2628363 |
0.55 % |
146776 |
1.89 % |
| qd2 |
1663368 |
0.34 % |
1564799 |
0.33 % |
98569 |
1.27 % |
| qd2,mq40 |
60319 |
0.01 % |
50931 |
0.01 % |
9388 |
0.12 % |
| qd2,fs60,mq40 |
1006 |
0.00 % |
0 |
0.00 % |
1006 |
0.01 % |
| fs60 |
907 |
0.00 % |
0 |
0.00 % |
907 |
0.01 % |
| q20,qd2,fs60 |
761 |
0.00 % |
0 |
0.00 % |
761 |
0.01 % |
| qd2,fs60 |
722 |
0.00 % |
0 |
0.00 % |
722 |
0.01 % |
| fs60,mq40 |
433 |
0.00 % |
0 |
0.00 % |
433 |
0.01 % |
| q20,qd2,fs60,mq40 |
241 |
0.00 % |
0 |
0.00 % |
241 |
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 |
3924983 |
28.87 % |
| Transition |
G>A |
All |
1601176 |
11.78 % |
| Transition |
T>C |
All |
3840703 |
28.25 % |
| Transition |
C>T |
All |
1579362 |
11.62 % |
| Transversion |
A>C |
All |
212121 |
1.56 % |
| Transversion |
C>A |
All |
540303 |
3.97 % |
| Transversion |
T>G |
All |
217729 |
1.60 % |
| Transversion |
G>T |
All |
529763 |
3.90 % |
| Transversion |
A>T |
All |
375162 |
2.76 % |
| Transversion |
T>A |
All |
365520 |
2.69 % |
| Transversion |
C>G |
All |
205882 |
1.51 % |
| Transversion |
G>C |
All |
201515 |
1.48 % |
| |
|
|
|
|
| Transition |
A>G |
Passed |
392574 |
18.54 % |
| Transition |
G>A |
Passed |
350008 |
16.53 % |
| Transition |
T>C |
Passed |
390775 |
18.45 % |
| Transition |
C>T |
Passed |
351629 |
16.61 % |
| Transversion |
A>C |
Passed |
82862 |
3.91 % |
| Transversion |
C>A |
Passed |
78930 |
3.73 % |
| Transversion |
T>G |
Passed |
82416 |
3.89 % |
| Transversion |
G>T |
Passed |
78125 |
3.69 % |
| Transversion |
A>T |
Passed |
55718 |
2.63 % |
| Transversion |
T>A |
Passed |
55650 |
2.63 % |
| Transversion |
C>G |
Passed |
99213 |
4.69 % |
| Transversion |
G>C |
Passed |
99708 |
4.71 % |
| |
|
|
|
|
| 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 |
4.13 |
10946224 |
2647995 |
| Passed |
2.35 |
1484986 |
632622 |
| dbSNPAll |
0 |
0 |
0 |
| dbSNPPassed |
0 |
0 |
0 |