/EXTERNAL BLUEPRINT/variants/K006388_K006401_24_lane_gembs
BACK
SAMPLE K006388_K006401_24_lane_gembs
Variant counts
| Type |
Total |
Pass |
% |
| SNPs |
1152196867 |
1034200827 |
89.76 % |
| Multiallelic |
0 |
0 |
0.00 % |
VCF Filtering Stats
| Type |
#Sites |
% |
#Non-Variant Sites |
% |
#Variant Sites |
% |
| All |
1152196867 |
100% |
1141172827 |
99.04 % |
11024040 |
0.96 % |
| |
|
|
|
|
|
|
| Passed |
1035264656 |
89.85 % |
1031769705 |
90.41 % |
3494951 |
0.34 % |
| Filtered |
116932211 |
10.15 % |
109403122 |
9.59 % |
7529089 |
0.73 % |
| |
|
|
|
|
|
|
| q20 |
79101032 |
67.65 % |
78271917 |
71.54 % |
829115 |
11.01 % |
| q20,mq40 |
11288279 |
9.65 % |
11186262 |
10.22 % |
102017 |
1.35 % |
| q20,qd2 |
9327029 |
7.98 % |
3314365 |
3.03 % |
6012664 |
79.86 % |
| qd2 |
7338094 |
6.28 % |
7178856 |
6.56 % |
159238 |
2.11 % |
| mq40 |
7013182 |
6.00 % |
6801982 |
6.22 % |
211200 |
2.81 % |
| q20,qd2,mq40 |
2729617 |
2.33 % |
2546402 |
2.33 % |
183215 |
2.43 % |
| qd2,mq40 |
121213 |
0.10 % |
103338 |
0.09 % |
17875 |
0.24 % |
| fs60 |
3964 |
0.00 % |
0 |
0.00 % |
3964 |
0.05 % |
| qd2,fs60 |
3160 |
0.00 % |
0 |
0.00 % |
3160 |
0.04 % |
| q20,qd2,fs60 |
2713 |
0.00 % |
0 |
0.00 % |
2713 |
0.04 % |
| qd2,fs60,mq40 |
2631 |
0.00 % |
0 |
0.00 % |
2631 |
0.03 % |
| fs60,mq40 |
928 |
0.00 % |
0 |
0.00 % |
928 |
0.01 % |
| q20,qd2,fs60,mq40 |
366 |
0.00 % |
0 |
0.00 % |
366 |
0.00 % |
| q20,fs60 |
2 |
0.00 % |
0 |
0.00 % |
2 |
0.00 % |
| q20,fs60,mq40 |
1 |
0.00 % |
0 |
0.00 % |
1 |
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 |
4094293 |
31.96 % |
| Transition |
G>A |
All |
1115431 |
8.71 % |
| Transition |
T>C |
All |
4058104 |
31.68 % |
| Transition |
C>T |
All |
1128721 |
8.81 % |
| Transversion |
A>C |
All |
214578 |
1.67 % |
| Transversion |
C>A |
All |
444085 |
3.47 % |
| Transversion |
T>G |
All |
218438 |
1.71 % |
| Transversion |
G>T |
All |
442577 |
3.45 % |
| Transversion |
A>T |
All |
351072 |
2.74 % |
| Transversion |
T>A |
All |
340019 |
2.65 % |
| Transversion |
C>G |
All |
202602 |
1.58 % |
| Transversion |
G>C |
All |
200707 |
1.57 % |
| |
|
|
|
|
| Transition |
A>G |
Passed |
613855 |
17.22 % |
| Transition |
G>A |
Passed |
587840 |
16.49 % |
| Transition |
T>C |
Passed |
614679 |
17.25 % |
| Transition |
C>T |
Passed |
591943 |
16.61 % |
| Transversion |
A>C |
Passed |
149659 |
4.20 % |
| Transversion |
C>A |
Passed |
150818 |
4.23 % |
| Transversion |
T>G |
Passed |
150261 |
4.22 % |
| Transversion |
G>T |
Passed |
151371 |
4.25 % |
| Transversion |
A>T |
Passed |
127723 |
3.58 % |
| Transversion |
T>A |
Passed |
127577 |
3.58 % |
| Transversion |
C>G |
Passed |
148794 |
4.17 % |
| Transversion |
G>C |
Passed |
149581 |
4.20 % |
| |
|
|
|
|
| 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 |
4.31 |
10396549 |
2414078 |
| Passed |
2.08 |
2408317 |
1155784 |
| dbSNPAll |
0 |
0 |
0 |
| dbSNPPassed |
0 |
0 |
0 |