/EXTERNAL BLUEPRINT/variants/K006421_12_lane_gembs
BACK
SAMPLE K006421_12_lane_gembs
Variant counts
| Type |
Total |
Pass |
% |
| SNPs |
1157284210 |
1029383727 |
88.95 % |
| Multiallelic |
0 |
0 |
0.00 % |
VCF Filtering Stats
| Type |
#Sites |
% |
#Non-Variant Sites |
% |
#Variant Sites |
% |
| All |
1157284210 |
100% |
1144714145 |
98.91 % |
12570065 |
1.09 % |
| |
|
|
|
|
|
|
| Passed |
1030441537 |
89.04 % |
1026952508 |
89.71 % |
3489029 |
0.34 % |
| Filtered |
126842673 |
10.96 % |
117761637 |
10.29 % |
9081036 |
0.88 % |
| |
|
|
|
|
|
|
| q20 |
93176102 |
73.46 % |
92375243 |
78.44 % |
800859 |
8.82 % |
| q20,mq40 |
12956146 |
10.21 % |
12851376 |
10.91 % |
104770 |
1.15 % |
| q20,qd2 |
12251002 |
9.66 % |
4584680 |
3.89 % |
7666322 |
84.42 % |
| mq40 |
3583460 |
2.83 % |
3391080 |
2.88 % |
192380 |
2.12 % |
| q20,qd2,mq40 |
3129881 |
2.47 % |
2949871 |
2.50 % |
180010 |
1.98 % |
| qd2 |
1703923 |
1.34 % |
1575922 |
1.34 % |
128001 |
1.41 % |
| qd2,mq40 |
41105 |
0.03 % |
33465 |
0.03 % |
7640 |
0.08 % |
| qd2,fs60,mq40 |
518 |
0.00 % |
0 |
0.00 % |
518 |
0.01 % |
| fs60,mq40 |
261 |
0.00 % |
0 |
0.00 % |
261 |
0.00 % |
| qd2,fs60 |
141 |
0.00 % |
0 |
0.00 % |
141 |
0.00 % |
| q20,qd2,fs60,mq40 |
60 |
0.00 % |
0 |
0.00 % |
60 |
0.00 % |
| fs60 |
52 |
0.00 % |
0 |
0.00 % |
52 |
0.00 % |
| q20,qd2,fs60 |
20 |
0.00 % |
0 |
0.00 % |
20 |
0.00 % |
| q20,fs60,mq40 |
2 |
0.00 % |
0 |
0.00 % |
2 |
0.00 % |
| q20,fs60 |
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 |
4649380 |
32.70 % |
| Transition |
G>A |
All |
954185 |
6.71 % |
| Transition |
T>C |
All |
4618223 |
32.48 % |
| Transition |
C>T |
All |
957843 |
6.74 % |
| Transversion |
A>C |
All |
215786 |
1.52 % |
| Transversion |
C>A |
All |
629578 |
4.43 % |
| Transversion |
T>G |
All |
216978 |
1.53 % |
| Transversion |
G>T |
All |
618365 |
4.35 % |
| Transversion |
A>T |
All |
477330 |
3.36 % |
| Transversion |
T>A |
All |
474584 |
3.34 % |
| Transversion |
C>G |
All |
203327 |
1.43 % |
| Transversion |
G>C |
All |
204714 |
1.44 % |
| |
|
|
|
|
| Transition |
A>G |
Passed |
617584 |
17.24 % |
| Transition |
G>A |
Passed |
581098 |
16.22 % |
| Transition |
T>C |
Passed |
619528 |
17.29 % |
| Transition |
C>T |
Passed |
584334 |
16.31 % |
| Transversion |
A>C |
Passed |
150556 |
4.20 % |
| Transversion |
C>A |
Passed |
156165 |
4.36 % |
| Transversion |
T>G |
Passed |
150685 |
4.21 % |
| Transversion |
G>T |
Passed |
156508 |
4.37 % |
| Transversion |
A>T |
Passed |
133162 |
3.72 % |
| Transversion |
T>A |
Passed |
133833 |
3.74 % |
| Transversion |
C>G |
Passed |
149329 |
4.17 % |
| Transversion |
G>C |
Passed |
150120 |
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 |
3.68 |
11179631 |
3040662 |
| Passed |
2.04 |
2402544 |
1180358 |
| dbSNPAll |
0 |
0 |
0 |
| dbSNPPassed |
0 |
0 |
0 |