/EXTERNAL BLUEPRINT/variants/K006333_15_lane_gembs
BACK
SAMPLE K006333_15_lane_gembs
Variant counts
| Type |
Total |
Pass |
% |
| SNPs |
1132957524 |
720413914 |
63.59 % |
| Multiallelic |
0 |
0 |
0.00 % |
VCF Filtering Stats
| Type |
#Sites |
% |
#Non-Variant Sites |
% |
#Variant Sites |
% |
| All |
1132957524 |
100% |
1113401909 |
98.27 % |
19555615 |
1.73 % |
| |
|
|
|
|
|
|
| Passed |
722438510 |
63.77 % |
718894518 |
64.57 % |
3543992 |
0.49 % |
| Filtered |
410519014 |
36.23 % |
394507391 |
35.43 % |
16011623 |
2.22 % |
| |
|
|
|
|
|
|
| q20 |
341447262 |
83.17 % |
339596377 |
86.08 % |
1850885 |
11.56 % |
| q20,qd2 |
42724948 |
10.41 % |
29224565 |
7.41 % |
13500383 |
84.32 % |
| q20,mq40 |
13755545 |
3.35 % |
13643583 |
3.46 % |
111962 |
0.70 % |
| mq40 |
7169952 |
1.75 % |
6987358 |
1.77 % |
182594 |
1.14 % |
| q20,qd2,mq40 |
3079663 |
0.75 % |
2863455 |
0.73 % |
216208 |
1.35 % |
| qd2 |
2231351 |
0.54 % |
2104701 |
0.53 % |
126650 |
0.79 % |
| qd2,mq40 |
100324 |
0.02 % |
87352 |
0.02 % |
12972 |
0.08 % |
| q20,qd2,fs60 |
3409 |
0.00 % |
0 |
0.00 % |
3409 |
0.02 % |
| fs60 |
2162 |
0.00 % |
0 |
0.00 % |
2162 |
0.01 % |
| qd2,fs60,mq40 |
1732 |
0.00 % |
0 |
0.00 % |
1732 |
0.01 % |
| qd2,fs60 |
1520 |
0.00 % |
0 |
0.00 % |
1520 |
0.01 % |
| q20,qd2,fs60,mq40 |
577 |
0.00 % |
0 |
0.00 % |
577 |
0.00 % |
| fs60,mq40 |
565 |
0.00 % |
0 |
0.00 % |
565 |
0.00 % |
| q20,fs60 |
3 |
0.00 % |
0 |
0.00 % |
3 |
0.00 % |
| q20,fs60,mq40 |
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 |
3934674 |
16.03 % |
| Transition |
G>A |
All |
7121410 |
29.02 % |
| Transition |
T>C |
All |
3640436 |
14.84 % |
| Transition |
C>T |
All |
6954126 |
28.34 % |
| Transversion |
A>C |
All |
223572 |
0.91 % |
| Transversion |
C>A |
All |
571895 |
2.33 % |
| Transversion |
T>G |
All |
244848 |
1.00 % |
| Transversion |
G>T |
All |
561890 |
2.29 % |
| Transversion |
A>T |
All |
445649 |
1.82 % |
| Transversion |
T>A |
All |
446521 |
1.82 % |
| Transversion |
C>G |
All |
201348 |
0.82 % |
| Transversion |
G>C |
All |
191883 |
0.78 % |
| |
|
|
|
|
| Transition |
A>G |
Passed |
427145 |
18.95 % |
| Transition |
G>A |
Passed |
376864 |
16.72 % |
| Transition |
T>C |
Passed |
425323 |
18.87 % |
| Transition |
C>T |
Passed |
378440 |
16.79 % |
| Transversion |
A>C |
Passed |
86157 |
3.82 % |
| Transversion |
C>A |
Passed |
80035 |
3.55 % |
| Transversion |
T>G |
Passed |
85886 |
3.81 % |
| Transversion |
G>T |
Passed |
79953 |
3.55 % |
| Transversion |
A>T |
Passed |
56922 |
2.53 % |
| Transversion |
T>A |
Passed |
57059 |
2.53 % |
| Transversion |
C>G |
Passed |
99939 |
4.43 % |
| Transversion |
G>C |
Passed |
100266 |
4.45 % |
| |
|
|
|
|
| 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 |
7.50 |
21650646 |
2887606 |
| Passed |
2.49 |
1607772 |
646217 |
| dbSNPAll |
0 |
0 |
0 |
| dbSNPPassed |
0 |
0 |
0 |