/EXTERNAL DEEP/variants/K006045_K006046_K006047_K006048_K006049_K006049_K006050_6_lane_gembs
BACK
SAMPLE K006045_K006046_K006047_K006048_K006049_K006049_K006050_6_lane_gembs
Variant counts
| Type |
Total |
Pass |
% |
| SNPs |
1197471599 |
861084926 |
71.91 % |
| Multiallelic |
0 |
0 |
0.00 % |
VCF Filtering Stats
| Type |
#Sites |
% |
#Non-Variant Sites |
% |
#Variant Sites |
% |
| All |
1197471599 |
100% |
1139701932 |
95.18 % |
57769667 |
4.82 % |
| |
|
|
|
|
|
|
| Passed |
868766481 |
72.55 % |
855749640 |
75.09 % |
13016841 |
1.50 % |
| Filtered |
328705118 |
27.45 % |
283952292 |
24.91 % |
44752826 |
5.15 % |
| |
|
|
|
|
|
|
| q20 |
258659894 |
78.69 % |
250304533 |
88.15 % |
8355361 |
18.67 % |
| q20,qd2 |
48015388 |
14.61 % |
13447465 |
4.74 % |
34567923 |
77.24 % |
| q20,mq40 |
11483263 |
3.49 % |
11210797 |
3.95 % |
272466 |
0.61 % |
| qd2 |
5563893 |
1.69 % |
4570190 |
1.61 % |
993703 |
2.22 % |
| q20,qd2,mq40 |
3641776 |
1.11 % |
3413657 |
1.20 % |
228119 |
0.51 % |
| mq40 |
1316622 |
0.40 % |
986628 |
0.35 % |
329994 |
0.74 % |
| qd2,mq40 |
23821 |
0.01 % |
19022 |
0.01 % |
4799 |
0.01 % |
| qd2,fs60,mq40 |
176 |
0.00 % |
0 |
0.00 % |
176 |
0.00 % |
| qd2,fs60 |
86 |
0.00 % |
0 |
0.00 % |
86 |
0.00 % |
| fs60,mq40 |
86 |
0.00 % |
0 |
0.00 % |
86 |
0.00 % |
| fs60 |
50 |
0.00 % |
0 |
0.00 % |
50 |
0.00 % |
| q20,qd2,fs60 |
36 |
0.00 % |
0 |
0.00 % |
36 |
0.00 % |
| q20,qd2,fs60,mq40 |
27 |
0.00 % |
0 |
0.00 % |
27 |
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 |
23293250 |
38.93 % |
| Transition |
G>A |
All |
3008289 |
5.03 % |
| Transition |
T>C |
All |
24166789 |
40.39 % |
| Transition |
C>T |
All |
2327857 |
3.89 % |
| Transversion |
A>C |
All |
536840 |
0.90 % |
| Transversion |
C>A |
All |
1575978 |
2.63 % |
| Transversion |
T>G |
All |
609363 |
1.02 % |
| Transversion |
G>T |
All |
1522093 |
2.54 % |
| Transversion |
A>T |
All |
848720 |
1.42 % |
| Transversion |
T>A |
All |
932797 |
1.56 % |
| Transversion |
C>G |
All |
519227 |
0.87 % |
| Transversion |
G>C |
All |
494620 |
0.83 % |
| |
|
|
|
|
| Transition |
A>G |
Passed |
1678153 |
26.76 % |
| Transition |
G>A |
Passed |
614777 |
9.80 % |
| Transition |
T>C |
Passed |
2086614 |
33.27 % |
| Transition |
C>T |
Passed |
556906 |
8.88 % |
| Transversion |
A>C |
Passed |
153113 |
2.44 % |
| Transversion |
C>A |
Passed |
218234 |
3.48 % |
| Transversion |
T>G |
Passed |
164782 |
2.63 % |
| Transversion |
G>T |
Passed |
204234 |
3.26 % |
| Transversion |
A>T |
Passed |
134447 |
2.14 % |
| Transversion |
T>A |
Passed |
150245 |
2.40 % |
| Transversion |
C>G |
Passed |
156707 |
2.50 % |
| Transversion |
G>C |
Passed |
153587 |
2.45 % |
| |
|
|
|
|
| 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 |
7.50 |
52796185 |
7039638 |
| Passed |
3.70 |
4936450 |
1335349 |
| dbSNPAll |
0 |
0 |
0 |
| dbSNPPassed |
0 |
0 |
0 |