/EXTERNAL BLUEPRINT/variants/K012022_K012023_K012024_K012025_K012026_K012027_K012028_K012029_K012030_K012031_K012032_11_lane_gembs
BACK
SAMPLE K012022_K012023_K012024_K012025_K012026_K012027_K012028_K012029_K012030_K012031_K012032_11_lane_gembs
Variant counts
| Type |
Total |
Pass |
% |
| SNPs |
903793050 |
6681877 |
0.74 % |
| Multiallelic |
0 |
0 |
0.00 % |
VCF Filtering Stats
| Type |
#Sites |
% |
#Non-Variant Sites |
% |
#Variant Sites |
% |
| All |
903793050 |
100% |
884700535 |
97.89 % |
19092515 |
2.11 % |
| |
|
|
|
|
|
|
| Passed |
16571437 |
1.83 % |
6153748 |
0.70 % |
10417689 |
62.87 % |
| Filtered |
887221613 |
98.17 % |
878546787 |
99.30 % |
8674826 |
52.35 % |
| |
|
|
|
|
|
|
| q20 |
697837123 |
78.65 % |
691988138 |
78.77 % |
5848985 |
67.42 % |
| q20,qd2 |
110439734 |
12.45 % |
108699366 |
12.37 % |
1740368 |
20.06 % |
| q20,mq40 |
57807755 |
6.52 % |
57412422 |
6.53 % |
395333 |
4.56 % |
| q20,qd2,mq40 |
20420702 |
2.30 % |
20316448 |
2.31 % |
104254 |
1.20 % |
| mq40 |
709219 |
0.08 % |
123926 |
0.01 % |
585293 |
6.75 % |
| qd2 |
5411 |
0.00 % |
5150 |
0.00 % |
261 |
0.00 % |
| qd2,mq40 |
1632 |
0.00 % |
1337 |
0.00 % |
295 |
0.00 % |
| fs60,mq40 |
18 |
0.00 % |
0 |
0.00 % |
18 |
0.00 % |
| qd2,fs60 |
8 |
0.00 % |
0 |
0.00 % |
8 |
0.00 % |
| fs60 |
5 |
0.00 % |
0 |
0.00 % |
5 |
0.00 % |
| qd2,fs60,mq40 |
3 |
0.00 % |
0 |
0.00 % |
3 |
0.00 % |
| q20,qd2,fs60,mq40 |
3 |
0.00 % |
0 |
0.00 % |
3 |
0.00 % |
| q20,fs60 |
0 |
0.00 % |
0 |
0.00 % |
0 |
0.00 % |
| q20,qd2,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 |
5183512 |
21.91 % |
| Transition |
G>A |
All |
1897486 |
8.02 % |
| Transition |
T>C |
All |
6457224 |
27.29 % |
| Transition |
C>T |
All |
883431 |
3.73 % |
| Transversion |
A>C |
All |
817756 |
3.46 % |
| Transversion |
C>A |
All |
1614742 |
6.82 % |
| Transversion |
T>G |
All |
967964 |
4.09 % |
| Transversion |
G>T |
All |
1464198 |
6.19 % |
| Transversion |
A>T |
All |
1114894 |
4.71 % |
| Transversion |
T>A |
All |
1547202 |
6.54 % |
| Transversion |
C>G |
All |
784883 |
3.32 % |
| Transversion |
G>C |
All |
927594 |
3.92 % |
| |
|
|
|
|
| Transition |
A>G |
Passed |
90437 |
17.20 % |
| Transition |
G>A |
Passed |
69807 |
13.28 % |
| Transition |
T>C |
Passed |
140078 |
26.65 % |
| Transition |
C>T |
Passed |
31180 |
5.93 % |
| Transversion |
A>C |
Passed |
21492 |
4.09 % |
| Transversion |
C>A |
Passed |
30977 |
5.89 % |
| Transversion |
T>G |
Passed |
23737 |
4.52 % |
| Transversion |
G>T |
Passed |
19708 |
3.75 % |
| Transversion |
A>T |
Passed |
11633 |
2.21 % |
| Transversion |
T>A |
Passed |
29332 |
5.58 % |
| Transversion |
C>G |
Passed |
24356 |
4.63 % |
| Transversion |
G>C |
Passed |
32960 |
6.27 % |
| |
|
|
|
|
| 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 |
1.56 |
14421653 |
9239233 |
| Passed |
1.71 |
331502 |
194195 |
| dbSNPAll |
0 |
0 |
0 |
| dbSNPPassed |
0 |
0 |
0 |