/EXTERNAL BLUEPRINT/variants/K006385_K006398_19_lane_gembs
BACK
SAMPLE K006385_K006398_19_lane_gembs
Variant counts
| Type |
Total |
Pass |
% |
| SNPs |
1152390127 |
1025483353 |
88.99 % |
| Multiallelic |
0 |
0 |
0.00 % |
VCF Filtering Stats
| Type |
#Sites |
% |
#Non-Variant Sites |
% |
#Variant Sites |
% |
| All |
1152390127 |
100% |
1141050273 |
99.02 % |
11339854 |
0.98 % |
| |
|
|
|
|
|
|
| Passed |
1026496067 |
89.08 % |
1023083722 |
89.66 % |
3412345 |
0.33 % |
| Filtered |
125894060 |
10.92 % |
117966551 |
10.34 % |
7927509 |
0.77 % |
| |
|
|
|
|
|
|
| q20 |
80612316 |
64.03 % |
79761892 |
67.61 % |
850424 |
10.73 % |
| qd2 |
14232397 |
11.31 % |
14070121 |
11.93 % |
162276 |
2.05 % |
| q20,mq40 |
11418815 |
9.07 % |
11322796 |
9.60 % |
96019 |
1.21 % |
| q20,qd2 |
9566400 |
7.60 % |
3146315 |
2.67 % |
6420085 |
80.98 % |
| mq40 |
7184868 |
5.71 % |
6988520 |
5.92 % |
196348 |
2.48 % |
| q20,qd2,mq40 |
2751124 |
2.19 % |
2581077 |
2.19 % |
170047 |
2.15 % |
| qd2,mq40 |
111809 |
0.09 % |
95830 |
0.08 % |
15979 |
0.20 % |
| qd2,fs60 |
4602 |
0.00 % |
0 |
0.00 % |
4602 |
0.06 % |
| fs60 |
4464 |
0.00 % |
0 |
0.00 % |
4464 |
0.06 % |
| q20,qd2,fs60 |
3018 |
0.00 % |
0 |
0.00 % |
3018 |
0.04 % |
| qd2,fs60,mq40 |
2867 |
0.00 % |
0 |
0.00 % |
2867 |
0.04 % |
| fs60,mq40 |
947 |
0.00 % |
0 |
0.00 % |
947 |
0.01 % |
| q20,qd2,fs60,mq40 |
427 |
0.00 % |
0 |
0.00 % |
427 |
0.01 % |
| q20,fs60 |
4 |
0.00 % |
0 |
0.00 % |
4 |
0.00 % |
| q20,fs60,mq40 |
2 |
0.00 % |
0 |
0.00 % |
2 |
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 |
4306570 |
32.83 % |
| Transition |
G>A |
All |
1069712 |
8.16 % |
| Transition |
T>C |
All |
4271652 |
32.57 % |
| Transition |
C>T |
All |
1076518 |
8.21 % |
| Transversion |
A>C |
All |
213483 |
1.63 % |
| Transversion |
C>A |
All |
429746 |
3.28 % |
| Transversion |
T>G |
All |
216343 |
1.65 % |
| Transversion |
G>T |
All |
423016 |
3.23 % |
| Transversion |
A>T |
All |
355923 |
2.71 % |
| Transversion |
T>A |
All |
352892 |
2.69 % |
| Transversion |
C>G |
All |
200420 |
1.53 % |
| Transversion |
G>C |
All |
199550 |
1.52 % |
| |
|
|
|
|
| Transition |
A>G |
Passed |
610870 |
17.31 % |
| Transition |
G>A |
Passed |
575983 |
16.32 % |
| Transition |
T>C |
Passed |
613208 |
17.37 % |
| Transition |
C>T |
Passed |
578651 |
16.40 % |
| Transversion |
A>C |
Passed |
149785 |
4.24 % |
| Transversion |
C>A |
Passed |
148863 |
4.22 % |
| Transversion |
T>G |
Passed |
149991 |
4.25 % |
| Transversion |
G>T |
Passed |
150208 |
4.26 % |
| Transversion |
A>T |
Passed |
128374 |
3.64 % |
| Transversion |
T>A |
Passed |
128193 |
3.63 % |
| Transversion |
C>G |
Passed |
147283 |
4.17 % |
| Transversion |
G>C |
Passed |
147998 |
4.19 % |
| |
|
|
|
|
| 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 |
4.48 |
10724452 |
2391373 |
| Passed |
2.07 |
2378712 |
1150695 |
| dbSNPAll |
0 |
0 |
0 |
| dbSNPPassed |
0 |
0 |
0 |