/EXTERNAL BLUEPRINT/variants/K010502_1_lane_gembs
BACK
SAMPLE K010502_1_lane_gembs
Variant counts
| Type |
Total |
Pass |
% |
| SNPs |
1155479990 |
595481128 |
51.54 % |
| Multiallelic |
0 |
0 |
0.00 % |
VCF Filtering Stats
| Type |
#Sites |
% |
#Non-Variant Sites |
% |
#Variant Sites |
% |
| All |
1155479990 |
100% |
1135347570 |
98.26 % |
20132420 |
1.74 % |
| |
|
|
|
|
|
|
| Passed |
599889607 |
51.92 % |
593521242 |
52.28 % |
6368365 |
1.06 % |
| Filtered |
555590383 |
48.08 % |
541826328 |
47.72 % |
13764055 |
2.29 % |
| |
|
|
|
|
|
|
| q20 |
513557316 |
92.43 % |
510885697 |
94.29 % |
2671619 |
19.41 % |
| q20,qd2 |
20930394 |
3.77 % |
10261239 |
1.89 % |
10669155 |
77.51 % |
| q20,mq40 |
15835194 |
2.85 % |
15721722 |
2.90 % |
113472 |
0.82 % |
| q20,qd2,mq40 |
3755450 |
0.68 % |
3614654 |
0.67 % |
140796 |
1.02 % |
| mq40 |
1142571 |
0.21 % |
988416 |
0.18 % |
154155 |
1.12 % |
| qd2 |
347637 |
0.06 % |
337248 |
0.06 % |
10389 |
0.08 % |
| qd2,mq40 |
21415 |
0.00 % |
17352 |
0.00 % |
4063 |
0.03 % |
| qd2,fs60,mq40 |
179 |
0.00 % |
0 |
0.00 % |
179 |
0.00 % |
| fs60,mq40 |
108 |
0.00 % |
0 |
0.00 % |
108 |
0.00 % |
| qd2,fs60 |
61 |
0.00 % |
0 |
0.00 % |
61 |
0.00 % |
| fs60 |
26 |
0.00 % |
0 |
0.00 % |
26 |
0.00 % |
| q20,qd2,fs60,mq40 |
25 |
0.00 % |
0 |
0.00 % |
25 |
0.00 % |
| q20,qd2,fs60 |
7 |
0.00 % |
0 |
0.00 % |
7 |
0.00 % |
| q20,fs60 |
0 |
0.00 % |
0 |
0.00 % |
0 |
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 |
6621787 |
30.36 % |
| Transition |
G>A |
All |
1164841 |
5.34 % |
| Transition |
T>C |
All |
6593455 |
30.23 % |
| Transition |
C>T |
All |
1144689 |
5.25 % |
| Transversion |
A>C |
All |
269376 |
1.24 % |
| Transversion |
C>A |
All |
1827980 |
8.38 % |
| Transversion |
T>G |
All |
275216 |
1.26 % |
| Transversion |
G>T |
All |
1805491 |
8.28 % |
| Transversion |
A>T |
All |
789640 |
3.62 % |
| Transversion |
T>A |
All |
801423 |
3.67 % |
| Transversion |
C>G |
All |
261424 |
1.20 % |
| Transversion |
G>C |
All |
254079 |
1.16 % |
| |
|
|
|
|
| Transition |
A>G |
Passed |
426965 |
16.62 % |
| Transition |
G>A |
Passed |
390350 |
15.19 % |
| Transition |
T>C |
Passed |
428976 |
16.70 % |
| Transition |
C>T |
Passed |
392266 |
15.27 % |
| Transversion |
A>C |
Passed |
119144 |
4.64 % |
| Transversion |
C>A |
Passed |
122191 |
4.76 % |
| Transversion |
T>G |
Passed |
119592 |
4.66 % |
| Transversion |
G>T |
Passed |
122646 |
4.77 % |
| Transversion |
A>T |
Passed |
104204 |
4.06 % |
| Transversion |
T>A |
Passed |
104753 |
4.08 % |
| Transversion |
C>G |
Passed |
118673 |
4.62 % |
| Transversion |
G>C |
Passed |
119340 |
4.65 % |
| |
|
|
|
|
| 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 |
2.47 |
15524772 |
6284629 |
| Passed |
1.76 |
1638557 |
930543 |
| dbSNPAll |
0 |
0 |
0 |
| dbSNPPassed |
0 |
0 |
0 |