/EXTERNAL BLUEPRINT/variants/K006312_19_lane_gembs
BACK
SAMPLE K006312_19_lane_gembs
Variant counts
| Type |
Total |
Pass |
% |
| SNPs |
1040736732 |
465237294 |
44.70 % |
| Multiallelic |
0 |
0 |
0.00 % |
VCF Filtering Stats
| Type |
#Sites |
% |
#Non-Variant Sites |
% |
#Variant Sites |
% |
| All |
1040736732 |
100% |
1024902600 |
98.48 % |
15834132 |
1.52 % |
| |
|
|
|
|
|
|
| Passed |
466814850 |
44.85 % |
464344716 |
45.31 % |
2470134 |
0.53 % |
| Filtered |
573921882 |
55.15 % |
560557884 |
54.69 % |
13363998 |
2.86 % |
| |
|
|
|
|
|
|
| q20 |
465775802 |
81.16 % |
463860170 |
82.75 % |
1915632 |
14.33 % |
| q20,qd2 |
68076827 |
11.86 % |
57115510 |
10.19 % |
10961317 |
82.02 % |
| q20,mq40 |
15646545 |
2.73 % |
15562030 |
2.78 % |
84515 |
0.63 % |
| qd2 |
13904252 |
2.42 % |
13810593 |
2.46 % |
93659 |
0.70 % |
| mq40 |
6893717 |
1.20 % |
6752543 |
1.20 % |
141174 |
1.06 % |
| q20,qd2,mq40 |
3516735 |
0.61 % |
3376206 |
0.60 % |
140529 |
1.05 % |
| qd2,mq40 |
92627 |
0.02 % |
80832 |
0.01 % |
11795 |
0.09 % |
| qd2,fs60 |
4678 |
0.00 % |
0 |
0.00 % |
4678 |
0.04 % |
| q20,qd2,fs60 |
4627 |
0.00 % |
0 |
0.00 % |
4627 |
0.03 % |
| fs60 |
2426 |
0.00 % |
0 |
0.00 % |
2426 |
0.02 % |
| qd2,fs60,mq40 |
2112 |
0.00 % |
0 |
0.00 % |
2112 |
0.02 % |
| q20,qd2,fs60,mq40 |
890 |
0.00 % |
0 |
0.00 % |
890 |
0.01 % |
| fs60,mq40 |
641 |
0.00 % |
0 |
0.00 % |
641 |
0.00 % |
| q20,fs60,mq40 |
2 |
0.00 % |
0 |
0.00 % |
2 |
0.00 % |
| q20,fs60 |
1 |
0.00 % |
0 |
0.00 % |
1 |
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 |
2845667 |
10.12 % |
| Transition |
G>A |
All |
10239884 |
36.41 % |
| Transition |
T>C |
All |
2493005 |
8.86 % |
| Transition |
C>T |
All |
10102903 |
35.92 % |
| Transversion |
A>C |
All |
197161 |
0.70 % |
| Transversion |
C>A |
All |
479966 |
1.71 % |
| Transversion |
T>G |
All |
230482 |
0.82 % |
| Transversion |
G>T |
All |
456969 |
1.62 % |
| Transversion |
A>T |
All |
342029 |
1.22 % |
| Transversion |
T>A |
All |
361026 |
1.28 % |
| Transversion |
C>G |
All |
196389 |
0.70 % |
| Transversion |
G>C |
All |
177026 |
0.63 % |
| |
|
|
|
|
| Transition |
A>G |
Passed |
263974 |
19.76 % |
| Transition |
G>A |
Passed |
229628 |
17.19 % |
| Transition |
T>C |
Passed |
262760 |
19.67 % |
| Transition |
C>T |
Passed |
229116 |
17.15 % |
| Transversion |
A>C |
Passed |
46814 |
3.50 % |
| Transversion |
C>A |
Passed |
40846 |
3.06 % |
| Transversion |
T>G |
Passed |
46521 |
3.48 % |
| Transversion |
G>T |
Passed |
41024 |
3.07 % |
| Transversion |
A>T |
Passed |
25027 |
1.87 % |
| Transversion |
T>A |
Passed |
24777 |
1.85 % |
| Transversion |
C>G |
Passed |
62802 |
4.70 % |
| Transversion |
G>C |
Passed |
62865 |
4.70 % |
| |
|
|
|
|
| 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 |
10.52 |
25681459 |
2441048 |
| Passed |
2.81 |
985478 |
350676 |
| dbSNPAll |
0 |
0 |
0 |
| dbSNPPassed |
0 |
0 |
0 |