/EXTERNAL BLUEPRINT/variants/K006292_10_lane_gembs
BACK
SAMPLE K006292_10_lane_gembs
Variant counts
| Type |
Total |
Pass |
% |
| SNPs |
1111411230 |
665232479 |
59.85 % |
| Multiallelic |
0 |
0 |
0.00 % |
VCF Filtering Stats
| Type |
#Sites |
% |
#Non-Variant Sites |
% |
#Variant Sites |
% |
| All |
1111411230 |
100% |
1092927777 |
98.34 % |
18483453 |
1.66 % |
| |
|
|
|
|
|
|
| Passed |
666824665 |
60.00 % |
663881967 |
60.74 % |
2942698 |
0.44 % |
| Filtered |
444586565 |
40.00 % |
429045810 |
39.26 % |
15540755 |
2.33 % |
| |
|
|
|
|
|
|
| q20 |
368877868 |
82.97 % |
367335569 |
85.62 % |
1542299 |
9.92 % |
| q20,qd2 |
49426334 |
11.12 % |
35961127 |
8.38 % |
13465207 |
86.64 % |
| q20,mq40 |
13982993 |
3.15 % |
13888143 |
3.24 % |
94850 |
0.61 % |
| mq40 |
6737797 |
1.52 % |
6575224 |
1.53 % |
162573 |
1.05 % |
| q20,qd2,mq40 |
3192794 |
0.72 % |
3024876 |
0.71 % |
167918 |
1.08 % |
| qd2 |
2273249 |
0.51 % |
2185414 |
0.51 % |
87835 |
0.57 % |
| qd2,mq40 |
87792 |
0.02 % |
75457 |
0.02 % |
12335 |
0.08 % |
| q20,qd2,fs60 |
2178 |
0.00 % |
0 |
0.00 % |
2178 |
0.01 % |
| fs60 |
1578 |
0.00 % |
0 |
0.00 % |
1578 |
0.01 % |
| qd2,fs60,mq40 |
1491 |
0.00 % |
0 |
0.00 % |
1491 |
0.01 % |
| qd2,fs60 |
1301 |
0.00 % |
0 |
0.00 % |
1301 |
0.01 % |
| fs60,mq40 |
604 |
0.00 % |
0 |
0.00 % |
604 |
0.00 % |
| q20,qd2,fs60,mq40 |
583 |
0.00 % |
0 |
0.00 % |
583 |
0.00 % |
| q20,fs60 |
2 |
0.00 % |
0 |
0.00 % |
2 |
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 |
3009731 |
12.30 % |
| Transition |
G>A |
All |
8038519 |
32.84 % |
| Transition |
T>C |
All |
2899148 |
11.84 % |
| Transition |
C>T |
All |
7885512 |
32.22 % |
| Transversion |
A>C |
All |
203230 |
0.83 % |
| Transversion |
C>A |
All |
554797 |
2.27 % |
| Transversion |
T>G |
All |
212385 |
0.87 % |
| Transversion |
G>T |
All |
544491 |
2.22 % |
| Transversion |
A>T |
All |
384849 |
1.57 % |
| Transversion |
T>A |
All |
377184 |
1.54 % |
| Transversion |
C>G |
All |
187213 |
0.76 % |
| Transversion |
G>C |
All |
179738 |
0.73 % |
| |
|
|
|
|
| Transition |
A>G |
Passed |
378440 |
18.70 % |
| Transition |
G>A |
Passed |
350088 |
17.30 % |
| Transition |
T>C |
Passed |
376838 |
18.62 % |
| Transition |
C>T |
Passed |
350326 |
17.31 % |
| Transversion |
A>C |
Passed |
75056 |
3.71 % |
| Transversion |
C>A |
Passed |
70006 |
3.46 % |
| Transversion |
T>G |
Passed |
74911 |
3.70 % |
| Transversion |
G>T |
Passed |
69592 |
3.44 % |
| Transversion |
A>T |
Passed |
48862 |
2.41 % |
| Transversion |
T>A |
Passed |
48333 |
2.39 % |
| Transversion |
C>G |
Passed |
90561 |
4.47 % |
| Transversion |
G>C |
Passed |
90756 |
4.48 % |
| |
|
|
|
|
| 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 |
8.26 |
21832910 |
2643887 |
| Passed |
2.56 |
1455692 |
568077 |
| dbSNPAll |
0 |
0 |
0 |
| dbSNPPassed |
0 |
0 |
0 |