/EXTERNAL BLUEPRINT/variants/K010370_1_lane_gembs
BACK
SAMPLE K010370_1_lane_gembs
Variant counts
| Type |
Total |
Pass |
% |
| SNPs |
793318759 |
7482038 |
0.94 % |
| Multiallelic |
0 |
0 |
0.00 % |
VCF Filtering Stats
| Type |
#Sites |
% |
#Non-Variant Sites |
% |
#Variant Sites |
% |
| All |
793318759 |
100% |
790123932 |
99.60 % |
3194827 |
0.40 % |
| |
|
|
|
|
|
|
| Passed |
9008430 |
1.14 % |
7371406 |
0.93 % |
1637024 |
18.17 % |
| Filtered |
784310329 |
98.86 % |
782752526 |
99.07 % |
1557803 |
17.29 % |
| |
|
|
|
|
|
|
| q20 |
604170925 |
77.03 % |
603371228 |
77.08 % |
799697 |
51.33 % |
| q20,qd2 |
155828202 |
19.87 % |
155196028 |
19.83 % |
632174 |
40.58 % |
| q20,mq40 |
15675495 |
2.00 % |
15626878 |
2.00 % |
48617 |
3.12 % |
| q20,qd2,mq40 |
8522242 |
1.09 % |
8491930 |
1.08 % |
30312 |
1.95 % |
| mq40 |
95212 |
0.01 % |
50188 |
0.01 % |
45024 |
2.89 % |
| qd2 |
11855 |
0.00 % |
10839 |
0.00 % |
1016 |
0.07 % |
| qd2,mq40 |
6296 |
0.00 % |
5435 |
0.00 % |
861 |
0.06 % |
| qd2,fs60,mq40 |
31 |
0.00 % |
0 |
0.00 % |
31 |
0.00 % |
| q20,qd2,fs60,mq40 |
25 |
0.00 % |
0 |
0.00 % |
25 |
0.00 % |
| fs60,mq40 |
18 |
0.00 % |
0 |
0.00 % |
18 |
0.00 % |
| qd2,fs60 |
13 |
0.00 % |
0 |
0.00 % |
13 |
0.00 % |
| fs60 |
11 |
0.00 % |
0 |
0.00 % |
11 |
0.00 % |
| q20,qd2,fs60 |
4 |
0.00 % |
0 |
0.00 % |
4 |
0.00 % |
| q20,fs60 |
0 |
0.00 % |
0 |
0.00 % |
0 |
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 |
1240911 |
25.13 % |
| Transition |
G>A |
All |
308186 |
6.24 % |
| Transition |
T>C |
All |
1208635 |
24.47 % |
| Transition |
C>T |
All |
306536 |
6.21 % |
| Transversion |
A>C |
All |
116529 |
2.36 % |
| Transversion |
C>A |
All |
437329 |
8.86 % |
| Transversion |
T>G |
All |
123868 |
2.51 % |
| Transversion |
G>T |
All |
435978 |
8.83 % |
| Transversion |
A>T |
All |
267918 |
5.43 % |
| Transversion |
T>A |
All |
266026 |
5.39 % |
| Transversion |
C>G |
All |
116431 |
2.36 % |
| Transversion |
G>C |
All |
110002 |
2.23 % |
| |
|
|
|
|
| Transition |
A>G |
Passed |
19982 |
17.45 % |
| Transition |
G>A |
Passed |
22321 |
19.50 % |
| Transition |
T>C |
Passed |
20041 |
17.50 % |
| Transition |
C>T |
Passed |
22353 |
19.52 % |
| Transversion |
A>C |
Passed |
3510 |
3.07 % |
| Transversion |
C>A |
Passed |
3710 |
3.24 % |
| Transversion |
T>G |
Passed |
3447 |
3.01 % |
| Transversion |
G>T |
Passed |
3756 |
3.28 % |
| Transversion |
A>T |
Passed |
1816 |
1.59 % |
| Transversion |
T>A |
Passed |
1869 |
1.63 % |
| Transversion |
C>G |
Passed |
5835 |
5.10 % |
| Transversion |
G>C |
Passed |
5850 |
5.11 % |
| |
|
|
|
|
| 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 |
1.64 |
3064268 |
1874081 |
| Passed |
2.84 |
84697 |
29793 |
| dbSNPAll |
0 |
0 |
0 |
| dbSNPPassed |
0 |
0 |
0 |