/EXTERNAL BLUEPRINT/variants/K010541_1_lane_gembs
BACK
SAMPLE K010541_1_lane_gembs
Variant counts
| Type |
Total |
Pass |
% |
| SNPs |
1077443318 |
564982162 |
52.44 % |
| Multiallelic |
0 |
0 |
0.00 % |
VCF Filtering Stats
| Type |
#Sites |
% |
#Non-Variant Sites |
% |
#Variant Sites |
% |
| All |
1077443318 |
100% |
1055653912 |
97.98 % |
21789406 |
2.02 % |
| |
|
|
|
|
|
|
| Passed |
567428073 |
52.66 % |
563704024 |
53.40 % |
3724049 |
0.66 % |
| Filtered |
510015245 |
47.34 % |
491949888 |
46.60 % |
18065357 |
3.18 % |
| |
|
|
|
|
|
|
| q20 |
414038175 |
81.18 % |
411683649 |
83.68 % |
2354526 |
13.03 % |
| q20,qd2 |
63409418 |
12.43 % |
48762604 |
9.91 % |
14646814 |
81.08 % |
| q20,mq40 |
16790369 |
3.29 % |
16569257 |
3.37 % |
221112 |
1.22 % |
| mq40 |
8147861 |
1.60 % |
7820922 |
1.59 % |
326939 |
1.81 % |
| q20,qd2,mq40 |
4150924 |
0.81 % |
3786022 |
0.77 % |
364902 |
2.02 % |
| qd2 |
3343438 |
0.66 % |
3215575 |
0.65 % |
127863 |
0.71 % |
| qd2,mq40 |
126344 |
0.02 % |
111859 |
0.02 % |
14485 |
0.08 % |
| q20,qd2,fs60 |
3064 |
0.00 % |
0 |
0.00 % |
3064 |
0.02 % |
| fs60 |
1950 |
0.00 % |
0 |
0.00 % |
1950 |
0.01 % |
| qd2,fs60 |
1349 |
0.00 % |
0 |
0.00 % |
1349 |
0.01 % |
| qd2,fs60,mq40 |
1277 |
0.00 % |
0 |
0.00 % |
1277 |
0.01 % |
| q20,qd2,fs60,mq40 |
595 |
0.00 % |
0 |
0.00 % |
595 |
0.00 % |
| fs60,mq40 |
480 |
0.00 % |
0 |
0.00 % |
480 |
0.00 % |
| q20,fs60 |
1 |
0.00 % |
0 |
0.00 % |
1 |
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 |
3960855 |
14.18 % |
| Transition |
G>A |
All |
8281466 |
29.66 % |
| Transition |
T>C |
All |
3456169 |
12.38 % |
| Transition |
C>T |
All |
8074939 |
28.92 % |
| Transversion |
A>C |
All |
298530 |
1.07 % |
| Transversion |
C>A |
All |
788652 |
2.82 % |
| Transversion |
T>G |
All |
343012 |
1.23 % |
| Transversion |
G>T |
All |
782989 |
2.80 % |
| Transversion |
A>T |
All |
699630 |
2.51 % |
| Transversion |
T>A |
All |
698808 |
2.50 % |
| Transversion |
C>G |
All |
282084 |
1.01 % |
| Transversion |
G>C |
All |
258517 |
0.93 % |
| |
|
|
|
|
| Transition |
A>G |
Passed |
372681 |
20.25 % |
| Transition |
G>A |
Passed |
308410 |
16.76 % |
| Transition |
T>C |
Passed |
364599 |
19.81 % |
| Transition |
C>T |
Passed |
308047 |
16.74 % |
| Transversion |
A>C |
Passed |
64695 |
3.51 % |
| Transversion |
C>A |
Passed |
57885 |
3.14 % |
| Transversion |
T>G |
Passed |
65079 |
3.54 % |
| Transversion |
G>T |
Passed |
58037 |
3.15 % |
| Transversion |
A>T |
Passed |
39287 |
2.13 % |
| Transversion |
T>A |
Passed |
39305 |
2.14 % |
| Transversion |
C>G |
Passed |
81294 |
4.42 % |
| Transversion |
G>C |
Passed |
81383 |
4.42 % |
| |
|
|
|
|
| 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 |
5.73 |
23773429 |
4152222 |
| Passed |
2.78 |
1353737 |
486965 |
| dbSNPAll |
0 |
0 |
0 |
| dbSNPPassed |
0 |
0 |
0 |