/EXTERNAL BLUEPRINT/variants/K010419_K010420_K010421_K010422_K010423_K010424_K010425_K010426_K010427_K010428_K010429_11_lane_gembs
BACK
SAMPLE K010419_K010420_K010421_K010422_K010423_K010424_K010425_K010426_K010427_K010428_K010429_11_lane_gembs
Variant counts
| Type |
Total |
Pass |
% |
| SNPs |
965316948 |
16293493 |
1.69 % |
| Multiallelic |
0 |
0 |
0.00 % |
VCF Filtering Stats
| Type |
#Sites |
% |
#Non-Variant Sites |
% |
#Variant Sites |
% |
| All |
965316948 |
100% |
940512339 |
97.43 % |
24804609 |
2.57 % |
| |
|
|
|
|
|
|
| Passed |
26793376 |
2.78 % |
15314631 |
1.63 % |
11478745 |
42.84 % |
| Filtered |
938523572 |
97.22 % |
925197708 |
98.37 % |
13325864 |
49.74 % |
| |
|
|
|
|
|
|
| q20 |
731827817 |
77.98 % |
722834955 |
78.13 % |
8992862 |
67.48 % |
| q20,qd2 |
120086396 |
12.80 % |
117254446 |
12.67 % |
2831950 |
21.25 % |
| q20,mq40 |
62386005 |
6.65 % |
61763571 |
6.68 % |
622434 |
4.67 % |
| q20,qd2,mq40 |
23211692 |
2.47 % |
23044500 |
2.49 % |
167192 |
1.25 % |
| mq40 |
1000738 |
0.11 % |
290768 |
0.03 % |
709970 |
5.33 % |
| qd2 |
8055 |
0.00 % |
7226 |
0.00 % |
829 |
0.01 % |
| qd2,mq40 |
2815 |
0.00 % |
2242 |
0.00 % |
573 |
0.00 % |
| fs60,mq40 |
22 |
0.00 % |
0 |
0.00 % |
22 |
0.00 % |
| qd2,fs60 |
14 |
0.00 % |
0 |
0.00 % |
14 |
0.00 % |
| fs60 |
8 |
0.00 % |
0 |
0.00 % |
8 |
0.00 % |
| qd2,fs60,mq40 |
6 |
0.00 % |
0 |
0.00 % |
6 |
0.00 % |
| q20,qd2,fs60,mq40 |
3 |
0.00 % |
0 |
0.00 % |
3 |
0.00 % |
| q20,qd2,fs60 |
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 |
6556849 |
22.60 % |
| Transition |
G>A |
All |
2363473 |
8.15 % |
| Transition |
T>C |
All |
8110593 |
27.95 % |
| Transition |
C>T |
All |
1044612 |
3.60 % |
| Transversion |
A>C |
All |
933012 |
3.22 % |
| Transversion |
C>A |
All |
1946811 |
6.71 % |
| Transversion |
T>G |
All |
1156662 |
3.99 % |
| Transversion |
G>T |
All |
1728861 |
5.96 % |
| Transversion |
A>T |
All |
1321109 |
4.55 % |
| Transversion |
T>A |
All |
1844243 |
6.36 % |
| Transversion |
C>G |
All |
935129 |
3.22 % |
| Transversion |
G>C |
All |
1075164 |
3.71 % |
| |
|
|
|
|
| Transition |
A>G |
Passed |
181375 |
18.57 % |
| Transition |
G>A |
Passed |
128428 |
13.15 % |
| Transition |
T>C |
Passed |
288183 |
29.50 % |
| Transition |
C>T |
Passed |
47970 |
4.91 % |
| Transversion |
A>C |
Passed |
36339 |
3.72 % |
| Transversion |
C>A |
Passed |
56549 |
5.79 % |
| Transversion |
T>G |
Passed |
41454 |
4.24 % |
| Transversion |
G>T |
Passed |
30819 |
3.15 % |
| Transversion |
A>T |
Passed |
19351 |
1.98 % |
| Transversion |
T>A |
Passed |
53963 |
5.52 % |
| Transversion |
C>G |
Passed |
39075 |
4.00 % |
| Transversion |
G>C |
Passed |
53443 |
5.47 % |
| |
|
|
|
|
| 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 |
1.65 |
18075527 |
10940991 |
| Passed |
1.95 |
645956 |
330993 |
| dbSNPAll |
0 |
0 |
0 |
| dbSNPPassed |
0 |
0 |
0 |