/EXTERNAL BLUEPRINT/variants/K006360_11_lane_gembs
BACK
SAMPLE K006360_11_lane_gembs
Variant counts
| Type |
Total |
Pass |
% |
| SNPs |
1055087592 |
480812584 |
45.57 % |
| Multiallelic |
0 |
0 |
0.00 % |
VCF Filtering Stats
| Type |
#Sites |
% |
#Non-Variant Sites |
% |
#Variant Sites |
% |
| All |
1055087592 |
100% |
1037784909 |
98.36 % |
17302683 |
1.64 % |
| |
|
|
|
|
|
|
| Passed |
482361232 |
45.72 % |
479881202 |
46.24 % |
2480030 |
0.51 % |
| Filtered |
572726360 |
54.28 % |
557903707 |
53.76 % |
14822653 |
3.07 % |
| |
|
|
|
|
|
|
| q20 |
467747185 |
81.67 % |
465864949 |
83.50 % |
1882236 |
12.70 % |
| q20,qd2 |
70213784 |
12.26 % |
57803605 |
10.36 % |
12410179 |
83.72 % |
| q20,mq40 |
16250329 |
2.84 % |
16150482 |
2.89 % |
99847 |
0.67 % |
| qd2 |
8211633 |
1.43 % |
8129321 |
1.46 % |
82312 |
0.56 % |
| mq40 |
6250430 |
1.09 % |
6111053 |
1.10 % |
139377 |
0.94 % |
| q20,qd2,mq40 |
3956179 |
0.69 % |
3770922 |
0.68 % |
185257 |
1.25 % |
| qd2,mq40 |
84263 |
0.01 % |
73375 |
0.01 % |
10888 |
0.07 % |
| q20,qd2,fs60 |
4830 |
0.00 % |
0 |
0.00 % |
4830 |
0.03 % |
| qd2,fs60 |
2954 |
0.00 % |
0 |
0.00 % |
2954 |
0.02 % |
| fs60 |
1995 |
0.00 % |
0 |
0.00 % |
1995 |
0.01 % |
| qd2,fs60,mq40 |
1485 |
0.00 % |
0 |
0.00 % |
1485 |
0.01 % |
| q20,qd2,fs60,mq40 |
887 |
0.00 % |
0 |
0.00 % |
887 |
0.01 % |
| fs60,mq40 |
401 |
0.00 % |
0 |
0.00 % |
401 |
0.00 % |
| q20,fs60 |
5 |
0.00 % |
0 |
0.00 % |
5 |
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 |
2768493 |
9.83 % |
| Transition |
G>A |
All |
10059937 |
35.74 % |
| Transition |
T>C |
All |
2439598 |
8.67 % |
| Transition |
C>T |
All |
9866288 |
35.05 % |
| Transversion |
A>C |
All |
242049 |
0.86 % |
| Transversion |
C>A |
All |
555761 |
1.97 % |
| Transversion |
T>G |
All |
277164 |
0.98 % |
| Transversion |
G>T |
All |
539870 |
1.92 % |
| Transversion |
A>T |
All |
488440 |
1.74 % |
| Transversion |
T>A |
All |
500134 |
1.78 % |
| Transversion |
C>G |
All |
216077 |
0.77 % |
| Transversion |
G>C |
All |
197526 |
0.70 % |
| |
|
|
|
|
| Transition |
A>G |
Passed |
256697 |
18.87 % |
| Transition |
G>A |
Passed |
246927 |
18.15 % |
| Transition |
T>C |
Passed |
256324 |
18.84 % |
| Transition |
C>T |
Passed |
246282 |
18.10 % |
| Transversion |
A>C |
Passed |
46608 |
3.43 % |
| Transversion |
C>A |
Passed |
42499 |
3.12 % |
| Transversion |
T>G |
Passed |
46558 |
3.42 % |
| Transversion |
G>T |
Passed |
42686 |
3.14 % |
| Transversion |
A>T |
Passed |
28025 |
2.06 % |
| Transversion |
T>A |
Passed |
27472 |
2.02 % |
| Transversion |
C>G |
Passed |
59852 |
4.40 % |
| Transversion |
G>C |
Passed |
60727 |
4.46 % |
| |
|
|
|
|
| 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 |
8.33 |
25134316 |
3017021 |
| Passed |
2.84 |
1006230 |
354427 |
| dbSNPAll |
0 |
0 |
0 |
| dbSNPPassed |
0 |
0 |
0 |