/EXTERNAL BLUEPRINT/variants/K006395_K006408_20_lane_gembs
BACK
SAMPLE K006395_K006408_20_lane_gembs
Variant counts
| Type |
Total |
Pass |
% |
| SNPs |
1153534354 |
1021679315 |
88.57 % |
| Multiallelic |
0 |
0 |
0.00 % |
VCF Filtering Stats
| Type |
#Sites |
% |
#Non-Variant Sites |
% |
#Variant Sites |
% |
| All |
1153534354 |
100% |
1142298349 |
99.03 % |
11236005 |
0.97 % |
| |
|
|
|
|
|
|
| Passed |
1022857315 |
88.67 % |
1019338259 |
89.24 % |
3519056 |
0.34 % |
| Filtered |
130677039 |
11.33 % |
122960090 |
10.76 % |
7716949 |
0.75 % |
| |
|
|
|
|
|
|
| q20 |
89910966 |
68.80 % |
89018139 |
72.40 % |
892827 |
11.57 % |
| q20,mq40 |
11251912 |
8.61 % |
11151460 |
9.07 % |
100452 |
1.30 % |
| qd2 |
10170764 |
7.78 % |
10001831 |
8.13 % |
168933 |
2.19 % |
| q20,qd2 |
9654890 |
7.39 % |
3521251 |
2.86 % |
6133639 |
79.48 % |
| mq40 |
6792093 |
5.20 % |
6582872 |
5.35 % |
209221 |
2.71 % |
| q20,qd2,mq40 |
2771510 |
2.12 % |
2590407 |
2.11 % |
181103 |
2.35 % |
| qd2,mq40 |
111275 |
0.09 % |
94130 |
0.08 % |
17145 |
0.22 % |
| fs60 |
3888 |
0.00 % |
0 |
0.00 % |
3888 |
0.05 % |
| qd2,fs60 |
3329 |
0.00 % |
0 |
0.00 % |
3329 |
0.04 % |
| q20,qd2,fs60 |
3029 |
0.00 % |
0 |
0.00 % |
3029 |
0.04 % |
| qd2,fs60,mq40 |
2195 |
0.00 % |
0 |
0.00 % |
2195 |
0.03 % |
| fs60,mq40 |
855 |
0.00 % |
0 |
0.00 % |
855 |
0.01 % |
| q20,qd2,fs60,mq40 |
327 |
0.00 % |
0 |
0.00 % |
327 |
0.00 % |
| q20,fs60,mq40 |
5 |
0.00 % |
0 |
0.00 % |
5 |
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 |
4226941 |
32.46 % |
| Transition |
G>A |
All |
1071285 |
8.23 % |
| Transition |
T>C |
All |
4193566 |
32.20 % |
| Transition |
C>T |
All |
1074926 |
8.25 % |
| Transversion |
A>C |
All |
216034 |
1.66 % |
| Transversion |
C>A |
All |
449479 |
3.45 % |
| Transversion |
T>G |
All |
219779 |
1.69 % |
| Transversion |
G>T |
All |
442874 |
3.40 % |
| Transversion |
A>T |
All |
363927 |
2.79 % |
| Transversion |
T>A |
All |
358776 |
2.76 % |
| Transversion |
C>G |
All |
203517 |
1.56 % |
| Transversion |
G>C |
All |
201089 |
1.54 % |
| |
|
|
|
|
| Transition |
A>G |
Passed |
599870 |
17.36 % |
| Transition |
G>A |
Passed |
562414 |
16.27 % |
| Transition |
T>C |
Passed |
602244 |
17.43 % |
| Transition |
C>T |
Passed |
564434 |
16.33 % |
| Transversion |
A>C |
Passed |
147142 |
4.26 % |
| Transversion |
C>A |
Passed |
145433 |
4.21 % |
| Transversion |
T>G |
Passed |
147495 |
4.27 % |
| Transversion |
G>T |
Passed |
145824 |
4.22 % |
| Transversion |
A>T |
Passed |
124701 |
3.61 % |
| Transversion |
T>A |
Passed |
123889 |
3.59 % |
| Transversion |
C>G |
Passed |
146167 |
4.23 % |
| Transversion |
G>C |
Passed |
146085 |
4.23 % |
| |
|
|
|
|
| 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 |
4.30 |
10566718 |
2455475 |
| Passed |
2.07 |
2328962 |
1126736 |
| dbSNPAll |
0 |
0 |
0 |
| dbSNPPassed |
0 |
0 |
0 |