/EXTERNAL BLUEPRINT/variants/K011800_K011850_33libs_33_lane_gembs
BACK
SAMPLE K011800_K011850_33libs_33_lane_gembs
Variant counts
| Type |
Total |
Pass |
% |
| SNPs |
1067032778 |
82474612 |
7.73 % |
| Multiallelic |
0 |
0 |
0.00 % |
VCF Filtering Stats
| Type |
#Sites |
% |
#Non-Variant Sites |
% |
#Variant Sites |
% |
| All |
1067032778 |
100% |
1028374667 |
96.38 % |
38658111 |
3.62 % |
| |
|
|
|
|
|
|
| Passed |
100232208 |
9.39 % |
79765940 |
7.76 % |
20466268 |
20.42 % |
| Filtered |
966800570 |
90.61 % |
948608727 |
92.24 % |
18191843 |
18.15 % |
| |
|
|
|
|
|
|
| q20 |
857643309 |
88.71 % |
847261723 |
89.32 % |
10381586 |
57.07 % |
| q20,mq40 |
56221332 |
5.82 % |
55692805 |
5.87 % |
528527 |
2.91 % |
| q20,qd2 |
41983149 |
4.34 % |
35832928 |
3.78 % |
6150221 |
33.81 % |
| q20,qd2,mq40 |
8998234 |
0.93 % |
8815344 |
0.93 % |
182890 |
1.01 % |
| mq40 |
1907994 |
0.20 % |
971465 |
0.10 % |
936529 |
5.15 % |
| qd2 |
42113 |
0.00 % |
31333 |
0.00 % |
10780 |
0.06 % |
| qd2,mq40 |
4331 |
0.00 % |
3129 |
0.00 % |
1202 |
0.01 % |
| fs60,mq40 |
52 |
0.00 % |
0 |
0.00 % |
52 |
0.00 % |
| qd2,fs60 |
18 |
0.00 % |
0 |
0.00 % |
18 |
0.00 % |
| qd2,fs60,mq40 |
18 |
0.00 % |
0 |
0.00 % |
18 |
0.00 % |
| fs60 |
14 |
0.00 % |
0 |
0.00 % |
14 |
0.00 % |
| q20,qd2,fs60,mq40 |
4 |
0.00 % |
0 |
0.00 % |
4 |
0.00 % |
| q20,qd2,fs60 |
2 |
0.00 % |
0 |
0.00 % |
2 |
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 |
9291661 |
22.23 % |
| Transition |
G>A |
All |
3302421 |
7.90 % |
| Transition |
T>C |
All |
12847879 |
30.74 % |
| Transition |
C>T |
All |
1556952 |
3.72 % |
| Transversion |
A>C |
All |
1495442 |
3.58 % |
| Transversion |
C>A |
All |
2349929 |
5.62 % |
| Transversion |
T>G |
All |
1509426 |
3.61 % |
| Transversion |
G>T |
All |
2114467 |
5.06 % |
| Transversion |
A>T |
All |
1859780 |
4.45 % |
| Transversion |
T>A |
All |
2560884 |
6.13 % |
| Transversion |
C>G |
All |
1311037 |
3.14 % |
| Transversion |
G>C |
All |
1601205 |
3.83 % |
| |
|
|
|
|
| Transition |
A>G |
Passed |
461427 |
16.97 % |
| Transition |
G>A |
Passed |
305868 |
11.25 % |
| Transition |
T>C |
Passed |
931210 |
34.26 % |
| Transition |
C>T |
Passed |
145543 |
5.35 % |
| Transversion |
A>C |
Passed |
121525 |
4.47 % |
| Transversion |
C>A |
Passed |
114514 |
4.21 % |
| Transversion |
T>G |
Passed |
108021 |
3.97 % |
| Transversion |
G>T |
Passed |
74651 |
2.75 % |
| Transversion |
A>T |
Passed |
66980 |
2.46 % |
| Transversion |
T>A |
Passed |
144208 |
5.30 % |
| Transversion |
C>G |
Passed |
101068 |
3.72 % |
| Transversion |
G>C |
Passed |
143401 |
5.28 % |
| |
|
|
|
|
| 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 |
1.82 |
26998913 |
14802170 |
| Passed |
2.11 |
1844048 |
874368 |
| dbSNPAll |
0 |
0 |
0 |
| dbSNPPassed |
0 |
0 |
0 |