/EXTERNAL BLUEPRINT/variants/K006427_18_lane_gembs
BACK
SAMPLE K006427_18_lane_gembs
Variant counts
| Type |
Total |
Pass |
% |
| SNPs |
1156965151 |
917611739 |
79.31 % |
| Multiallelic |
0 |
0 |
0.00 % |
VCF Filtering Stats
| Type |
#Sites |
% |
#Non-Variant Sites |
% |
#Variant Sites |
% |
| All |
1156965151 |
100% |
1142406479 |
98.74 % |
14558672 |
1.26 % |
| |
|
|
|
|
|
|
| Passed |
919870054 |
79.51 % |
915408304 |
80.13 % |
4461750 |
0.49 % |
| Filtered |
237095097 |
20.49 % |
226998175 |
19.87 % |
10096922 |
1.10 % |
| |
|
|
|
|
|
|
| q20 |
195235962 |
82.35 % |
193907675 |
85.42 % |
1328287 |
13.16 % |
| q20,qd2 |
16040676 |
6.77 % |
7860744 |
3.46 % |
8179932 |
81.01 % |
| q20,mq40 |
13571443 |
5.72 % |
13462251 |
5.93 % |
109192 |
1.08 % |
| qd2 |
4667589 |
1.97 % |
4592681 |
2.02 % |
74908 |
0.74 % |
| mq40 |
4428480 |
1.87 % |
4245357 |
1.87 % |
183123 |
1.81 % |
| q20,qd2,mq40 |
3097062 |
1.31 % |
2885137 |
1.27 % |
211925 |
2.10 % |
| qd2,mq40 |
52404 |
0.02 % |
44330 |
0.02 % |
8074 |
0.08 % |
| qd2,fs60,mq40 |
654 |
0.00 % |
0 |
0.00 % |
654 |
0.01 % |
| fs60,mq40 |
322 |
0.00 % |
0 |
0.00 % |
322 |
0.00 % |
| qd2,fs60 |
203 |
0.00 % |
0 |
0.00 % |
203 |
0.00 % |
| fs60 |
167 |
0.00 % |
0 |
0.00 % |
167 |
0.00 % |
| q20,qd2,fs60,mq40 |
90 |
0.00 % |
0 |
0.00 % |
90 |
0.00 % |
| q20,qd2,fs60 |
41 |
0.00 % |
0 |
0.00 % |
41 |
0.00 % |
| q20,fs60,mq40 |
4 |
0.00 % |
0 |
0.00 % |
4 |
0.00 % |
| q20,fs60 |
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 |
5069887 |
31.20 % |
| Transition |
G>A |
All |
1093427 |
6.73 % |
| Transition |
T>C |
All |
5005232 |
30.80 % |
| Transition |
C>T |
All |
1100861 |
6.77 % |
| Transversion |
A>C |
All |
217658 |
1.34 % |
| Transversion |
C>A |
All |
1118490 |
6.88 % |
| Transversion |
T>G |
All |
220411 |
1.36 % |
| Transversion |
G>T |
All |
1120015 |
6.89 % |
| Transversion |
A>T |
All |
449376 |
2.77 % |
| Transversion |
T>A |
All |
441315 |
2.72 % |
| Transversion |
C>G |
All |
207963 |
1.28 % |
| Transversion |
G>C |
All |
205571 |
1.27 % |
| |
|
|
|
|
| Transition |
A>G |
Passed |
549114 |
17.20 % |
| Transition |
G>A |
Passed |
522160 |
16.35 % |
| Transition |
T>C |
Passed |
549917 |
17.22 % |
| Transition |
C>T |
Passed |
525602 |
16.46 % |
| Transversion |
A>C |
Passed |
134228 |
4.20 % |
| Transversion |
C>A |
Passed |
136398 |
4.27 % |
| Transversion |
T>G |
Passed |
134551 |
4.21 % |
| Transversion |
G>T |
Passed |
137608 |
4.31 % |
| Transversion |
A>T |
Passed |
111243 |
3.48 % |
| Transversion |
T>A |
Passed |
111478 |
3.49 % |
| Transversion |
C>G |
Passed |
140350 |
4.40 % |
| Transversion |
G>C |
Passed |
140543 |
4.40 % |
| |
|
|
|
|
| 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 |
3.08 |
12269407 |
3980799 |
| Passed |
2.05 |
2146793 |
1046399 |
| dbSNPAll |
0 |
0 |
0 |
| dbSNPPassed |
0 |
0 |
0 |