/EXTERNAL BLUEPRINT/variants/K006269_11_lane_gembs
BACK
SAMPLE K006269_11_lane_gembs
Variant counts
| Type |
Total |
Pass |
% |
| SNPs |
1146328411 |
813226591 |
70.94 % |
| Multiallelic |
0 |
0 |
0.00 % |
VCF Filtering Stats
| Type |
#Sites |
% |
#Non-Variant Sites |
% |
#Variant Sites |
% |
| All |
1146328411 |
100% |
1131068924 |
98.67 % |
15259487 |
1.33 % |
| |
|
|
|
|
|
|
| Passed |
814296835 |
71.04 % |
811549536 |
71.75 % |
2747299 |
0.34 % |
| Filtered |
332031576 |
28.96 % |
319519388 |
28.25 % |
12512188 |
1.54 % |
| |
|
|
|
|
|
|
| q20 |
179727018 |
54.13 % |
177160647 |
55.45 % |
2566371 |
20.51 % |
| qd2 |
102768915 |
30.95 % |
102453893 |
32.07 % |
315022 |
2.52 % |
| q20,qd2 |
21686121 |
6.53 % |
12817218 |
4.01 % |
8868903 |
70.88 % |
| mq40 |
13083150 |
3.94 % |
12830295 |
4.02 % |
252855 |
2.02 % |
| q20,mq40 |
11746456 |
3.54 % |
11616448 |
3.64 % |
130008 |
1.04 % |
| q20,qd2,mq40 |
2715402 |
0.82 % |
2406289 |
0.75 % |
309113 |
2.47 % |
| qd2,mq40 |
263680 |
0.08 % |
234598 |
0.07 % |
29082 |
0.23 % |
| q20,qd2,fs60 |
17898 |
0.01 % |
0 |
0.00 % |
17898 |
0.14 % |
| qd2,fs60 |
8037 |
0.00 % |
0 |
0.00 % |
8037 |
0.06 % |
| fs60 |
6977 |
0.00 % |
0 |
0.00 % |
6977 |
0.06 % |
| qd2,fs60,mq40 |
4239 |
0.00 % |
0 |
0.00 % |
4239 |
0.03 % |
| fs60,mq40 |
2024 |
0.00 % |
0 |
0.00 % |
2024 |
0.02 % |
| q20,qd2,fs60,mq40 |
1617 |
0.00 % |
0 |
0.00 % |
1617 |
0.01 % |
| q20,fs60 |
25 |
0.00 % |
0 |
0.00 % |
25 |
0.00 % |
| q20,fs60,mq40 |
17 |
0.00 % |
0 |
0.00 % |
17 |
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 |
2940921 |
7.46 % |
| Transition |
G>A |
All |
15754378 |
39.94 % |
| Transition |
T>C |
All |
2773347 |
7.03 % |
| Transition |
C>T |
All |
15747674 |
39.92 % |
| Transversion |
A>C |
All |
204512 |
0.52 % |
| Transversion |
C>A |
All |
398153 |
1.01 % |
| Transversion |
T>G |
All |
214684 |
0.54 % |
| Transversion |
G>T |
All |
396069 |
1.00 % |
| Transversion |
A>T |
All |
318575 |
0.81 % |
| Transversion |
T>A |
All |
310722 |
0.79 % |
| Transversion |
C>G |
All |
197647 |
0.50 % |
| Transversion |
G>C |
All |
190672 |
0.48 % |
| |
|
|
|
|
| Transition |
A>G |
Passed |
502081 |
18.69 % |
| Transition |
G>A |
Passed |
441907 |
16.45 % |
| Transition |
T>C |
Passed |
500339 |
18.63 % |
| Transition |
C>T |
Passed |
439967 |
16.38 % |
| Transversion |
A>C |
Passed |
104922 |
3.91 % |
| Transversion |
C>A |
Passed |
100841 |
3.75 % |
| Transversion |
T>G |
Passed |
105013 |
3.91 % |
| Transversion |
G>T |
Passed |
100479 |
3.74 % |
| Transversion |
A>T |
Passed |
79131 |
2.95 % |
| Transversion |
T>A |
Passed |
79106 |
2.94 % |
| Transversion |
C>G |
Passed |
116439 |
4.33 % |
| Transversion |
G>C |
Passed |
116029 |
4.32 % |
| |
|
|
|
|
| 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 |
16.68 |
37216320 |
2231034 |
| Passed |
2.35 |
1884294 |
801960 |
| dbSNPAll |
0 |
0 |
0 |
| dbSNPPassed |
0 |
0 |
0 |