/EXTERNAL BLUEPRINT/variants/K011956_K011957_K011958_K011959_K011960_K011961_K011962_K011963_8_lane_gembs
BACK
SAMPLE K011956_K011957_K011958_K011959_K011960_K011961_K011962_K011963_8_lane_gembs
Variant counts
| Type |
Total |
Pass |
% |
| SNPs |
484762031 |
148137 |
0.03 % |
| Multiallelic |
0 |
0 |
0.00 % |
VCF Filtering Stats
| Type |
#Sites |
% |
#Non-Variant Sites |
% |
#Variant Sites |
% |
| All |
484762031 |
100% |
481756656 |
99.38 % |
3005375 |
0.62 % |
| |
|
|
|
|
|
|
| Passed |
1676481 |
0.35 % |
108185 |
0.02 % |
1568296 |
93.55 % |
| Filtered |
483085550 |
99.65 % |
481648471 |
99.98 % |
1437079 |
85.72 % |
| |
|
|
|
|
|
|
| q20 |
342377614 |
70.87 % |
341296169 |
70.86 % |
1081445 |
75.25 % |
| q20,qd2 |
97452704 |
20.17 % |
97295776 |
20.20 % |
156928 |
10.92 % |
| q20,mq40 |
30105755 |
6.23 % |
30018853 |
6.23 % |
86902 |
6.05 % |
| q20,qd2,mq40 |
13034646 |
2.70 % |
13019313 |
2.70 % |
15333 |
1.07 % |
| mq40 |
114018 |
0.02 % |
17662 |
0.00 % |
96356 |
6.70 % |
| qd2 |
501 |
0.00 % |
449 |
0.00 % |
52 |
0.00 % |
| qd2,mq40 |
305 |
0.00 % |
249 |
0.00 % |
56 |
0.00 % |
| fs60,mq40 |
4 |
0.00 % |
0 |
0.00 % |
4 |
0.00 % |
| fs60 |
1 |
0.00 % |
0 |
0.00 % |
1 |
0.00 % |
| q20,qd2,fs60 |
1 |
0.00 % |
0 |
0.00 % |
1 |
0.00 % |
| qd2,fs60,mq40 |
1 |
0.00 % |
0 |
0.00 % |
1 |
0.00 % |
| q20,fs60 |
0 |
0.00 % |
0 |
0.00 % |
0 |
0.00 % |
| qd2,fs60 |
0 |
0.00 % |
0 |
0.00 % |
0 |
0.00 % |
| q20,fs60,mq40 |
0 |
0.00 % |
0 |
0.00 % |
0 |
0.00 % |
| q20,qd2,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 |
1521888 |
21.75 % |
| Transition |
G>A |
All |
527849 |
7.55 % |
| Transition |
T>C |
All |
1973660 |
28.21 % |
| Transition |
C>T |
All |
278344 |
3.98 % |
| Transversion |
A>C |
All |
259065 |
3.70 % |
| Transversion |
C>A |
All |
441876 |
6.32 % |
| Transversion |
T>G |
All |
284907 |
4.07 % |
| Transversion |
G>T |
All |
409739 |
5.86 % |
| Transversion |
A>T |
All |
347217 |
4.96 % |
| Transversion |
T>A |
All |
464962 |
6.65 % |
| Transversion |
C>G |
All |
221508 |
3.17 % |
| Transversion |
G>C |
All |
264835 |
3.79 % |
| |
|
|
|
|
| Transition |
A>G |
Passed |
6443 |
16.29 % |
| Transition |
G>A |
Passed |
4805 |
12.15 % |
| Transition |
T>C |
Passed |
9129 |
23.08 % |
| Transition |
C>T |
Passed |
2407 |
6.09 % |
| Transversion |
A>C |
Passed |
1819 |
4.60 % |
| Transversion |
C>A |
Passed |
2575 |
6.51 % |
| Transversion |
T>G |
Passed |
1970 |
4.98 % |
| Transversion |
G>T |
Passed |
1960 |
4.96 % |
| Transversion |
A>T |
Passed |
1133 |
2.86 % |
| Transversion |
T>A |
Passed |
2382 |
6.02 % |
| Transversion |
C>G |
Passed |
2148 |
5.43 % |
| Transversion |
G>C |
Passed |
2782 |
7.03 % |
| |
|
|
|
|
| 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 |
1.60 |
4301741 |
2694109 |
| Passed |
1.36 |
22784 |
16769 |
| dbSNPAll |
0 |
0 |
0 |
| dbSNPPassed |
0 |
0 |
0 |