/EXTERNAL BLUEPRINT/variants/K011722_1_lane_gembs
BACK
SAMPLE K011722_1_lane_gembs
Variant counts
| Type |
Total |
Pass |
% |
| SNPs |
695280443 |
527431 |
0.08 % |
| Multiallelic |
0 |
0 |
0.00 % |
VCF Filtering Stats
| Type |
#Sites |
% |
#Non-Variant Sites |
% |
#Variant Sites |
% |
| All |
695280443 |
100% |
686957651 |
98.80 % |
8322792 |
1.20 % |
| |
|
|
|
|
|
|
| Passed |
4779229 |
0.69 % |
423333 |
0.06 % |
4355896 |
91.14 % |
| Filtered |
690501214 |
99.31 % |
686534318 |
99.94 % |
3966896 |
83.00 % |
| |
|
|
|
|
|
|
| q20 |
460233123 |
66.65 % |
457122541 |
66.58 % |
3110582 |
78.41 % |
| q20,qd2 |
170215570 |
24.65 % |
169821929 |
24.74 % |
393641 |
9.92 % |
| q20,mq40 |
38236345 |
5.54 % |
38041637 |
5.54 % |
194708 |
4.91 % |
| q20,qd2,mq40 |
21546481 |
3.12 % |
21517453 |
3.13 % |
29028 |
0.73 % |
| mq40 |
264983 |
0.04 % |
26226 |
0.00 % |
238757 |
6.02 % |
| qd2 |
4022 |
0.00 % |
3974 |
0.00 % |
48 |
0.00 % |
| qd2,mq40 |
653 |
0.00 % |
558 |
0.00 % |
95 |
0.00 % |
| qd2,fs60 |
14 |
0.00 % |
0 |
0.00 % |
14 |
0.00 % |
| fs60,mq40 |
10 |
0.00 % |
0 |
0.00 % |
10 |
0.00 % |
| fs60 |
8 |
0.00 % |
0 |
0.00 % |
8 |
0.00 % |
| q20,qd2,fs60,mq40 |
3 |
0.00 % |
0 |
0.00 % |
3 |
0.00 % |
| q20,qd2,fs60 |
1 |
0.00 % |
0 |
0.00 % |
1 |
0.00 % |
| q20,fs60,mq40 |
1 |
0.00 % |
0 |
0.00 % |
1 |
0.00 % |
| q20,fs60 |
0 |
0.00 % |
0 |
0.00 % |
0 |
0.00 % |
| qd2,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 |
2972481 |
23.18 % |
| Transition |
G>A |
All |
1009104 |
7.87 % |
| Transition |
T>C |
All |
3851519 |
30.03 % |
| Transition |
C>T |
All |
496150 |
3.87 % |
| Transversion |
A>C |
All |
474315 |
3.70 % |
| Transversion |
C>A |
All |
695854 |
5.43 % |
| Transversion |
T>G |
All |
586719 |
4.57 % |
| Transversion |
G>T |
All |
626712 |
4.89 % |
| Transversion |
A>T |
All |
504863 |
3.94 % |
| Transversion |
T>A |
All |
702009 |
5.47 % |
| Transversion |
C>G |
All |
418854 |
3.27 % |
| Transversion |
G>C |
All |
486761 |
3.80 % |
| |
|
|
|
|
| Transition |
A>G |
Passed |
15392 |
15.07 % |
| Transition |
G>A |
Passed |
14954 |
14.64 % |
| Transition |
T>C |
Passed |
28033 |
27.44 % |
| Transition |
C>T |
Passed |
6627 |
6.49 % |
| Transversion |
A>C |
Passed |
4351 |
4.26 % |
| Transversion |
C>A |
Passed |
5800 |
5.68 % |
| Transversion |
T>G |
Passed |
4526 |
4.43 % |
| Transversion |
G>T |
Passed |
3293 |
3.22 % |
| Transversion |
A>T |
Passed |
2214 |
2.17 % |
| Transversion |
T>A |
Passed |
5183 |
5.07 % |
| Transversion |
C>G |
Passed |
4770 |
4.67 % |
| Transversion |
G>C |
Passed |
7009 |
6.86 % |
| |
|
|
|
|
| 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 |
1.85 |
8329254 |
4496087 |
| Passed |
1.75 |
65006 |
37146 |
| dbSNPAll |
0 |
0 |
0 |
| dbSNPPassed |
0 |
0 |
0 |