/EXTERNAL BLUEPRINT/variants/K011973_K011977_K011978_K011979_K011980_K011981_K011982_K011983_K011984_K011985_K011986_K011987_K011988_K011989_K011990_K011991_K011992_K011993_K011994_K011995_K011996_K011997_22_lane_gembs
BACK
SAMPLE K011973_K011977_K011978_K011979_K011980_K011981_K011982_K011983_K011984_K011985_K011986_K011987_K011988_K011989_K011990_K011991_K011992_K011993_K011994_K011995_K011996_K011997_22_lane_gembs
Variant counts
| Type |
Total |
Pass |
% |
| SNPs |
685144050 |
891182 |
0.13 % |
| Multiallelic |
0 |
0 |
0.00 % |
VCF Filtering Stats
| Type |
#Sites |
% |
#Non-Variant Sites |
% |
#Variant Sites |
% |
| All |
685144050 |
100% |
677391525 |
98.87 % |
7752525 |
1.13 % |
| |
|
|
|
|
|
|
| Passed |
5197383 |
0.76 % |
741246 |
0.11 % |
4456137 |
85.74 % |
| Filtered |
679946667 |
99.24 % |
676650279 |
99.89 % |
3296388 |
63.42 % |
| |
|
|
|
|
|
|
| q20 |
536952705 |
78.97 % |
534487306 |
78.99 % |
2465399 |
74.79 % |
| q20,qd2 |
88127525 |
12.96 % |
87701567 |
12.96 % |
425958 |
12.92 % |
| q20,mq40 |
42349894 |
6.23 % |
42187132 |
6.23 % |
162762 |
4.94 % |
| q20,qd2,mq40 |
12258709 |
1.80 % |
12231944 |
1.81 % |
26765 |
0.81 % |
| mq40 |
252508 |
0.04 % |
37303 |
0.01 % |
215205 |
6.53 % |
| qd2 |
4518 |
0.00 % |
4412 |
0.00 % |
106 |
0.00 % |
| qd2,mq40 |
758 |
0.00 % |
615 |
0.00 % |
143 |
0.00 % |
| qd2,fs60 |
20 |
0.00 % |
0 |
0.00 % |
20 |
0.00 % |
| fs60,mq40 |
13 |
0.00 % |
0 |
0.00 % |
13 |
0.00 % |
| fs60 |
11 |
0.00 % |
0 |
0.00 % |
11 |
0.00 % |
| qd2,fs60,mq40 |
4 |
0.00 % |
0 |
0.00 % |
4 |
0.00 % |
| q20,qd2,fs60 |
1 |
0.00 % |
0 |
0.00 % |
1 |
0.00 % |
| q20,qd2,fs60,mq40 |
1 |
0.00 % |
0 |
0.00 % |
1 |
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 |
2696795 |
21.48 % |
| Transition |
G>A |
All |
944218 |
7.52 % |
| Transition |
T>C |
All |
3644817 |
29.03 % |
| Transition |
C>T |
All |
494589 |
3.94 % |
| Transversion |
A>C |
All |
523158 |
4.17 % |
| Transversion |
C>A |
All |
741677 |
5.91 % |
| Transversion |
T>G |
All |
513129 |
4.09 % |
| Transversion |
G>T |
All |
690345 |
5.50 % |
| Transversion |
A>T |
All |
618178 |
4.92 % |
| Transversion |
T>A |
All |
819219 |
6.53 % |
| Transversion |
C>G |
All |
392072 |
3.12 % |
| Transversion |
G>C |
All |
475886 |
3.79 % |
| |
|
|
|
|
| Transition |
A>G |
Passed |
22543 |
15.19 % |
| Transition |
G>A |
Passed |
18852 |
12.70 % |
| Transition |
T>C |
Passed |
36771 |
24.77 % |
| Transition |
C>T |
Passed |
9164 |
6.17 % |
| Transversion |
A>C |
Passed |
7332 |
4.94 % |
| Transversion |
C>A |
Passed |
8449 |
5.69 % |
| Transversion |
T>G |
Passed |
7298 |
4.92 % |
| Transversion |
G>T |
Passed |
6201 |
4.18 % |
| Transversion |
A>T |
Passed |
4347 |
2.93 % |
| Transversion |
T>A |
Passed |
9032 |
6.08 % |
| Transversion |
C>G |
Passed |
7924 |
5.34 % |
| Transversion |
G>C |
Passed |
10521 |
7.09 % |
| |
|
|
|
|
| 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 |
1.63 |
7780419 |
4773664 |
| Passed |
1.43 |
87330 |
61104 |
| dbSNPAll |
0 |
0 |
0 |
| dbSNPPassed |
0 |
0 |
0 |