/EXTERNAL KNIH/variants/K006247_1_lane_gembs
BACK
SAMPLE K006247_1_lane_gembs
Variant counts
| Type |
Total |
Pass |
% |
| SNPs |
1137729433 |
424127952 |
37.28 % |
| Multiallelic |
0 |
0 |
0.00 % |
VCF Filtering Stats
| Type |
#Sites |
% |
#Non-Variant Sites |
% |
#Variant Sites |
% |
| All |
1137729433 |
100% |
1084432860 |
95.32 % |
53296573 |
4.68 % |
| |
|
|
|
|
|
|
| Passed |
435502065 |
38.28 % |
417297124 |
38.48 % |
18204941 |
4.18 % |
| Filtered |
702227368 |
61.72 % |
667135736 |
61.52 % |
35091632 |
8.06 % |
| |
|
|
|
|
|
|
| q20 |
615667161 |
87.67 % |
601416871 |
90.15 % |
14250290 |
40.61 % |
| q20,qd2 |
74344068 |
10.59 % |
54463540 |
8.16 % |
19880528 |
56.65 % |
| q20,mq40 |
4993123 |
0.71 % |
4878421 |
0.73 % |
114702 |
0.33 % |
| qd2 |
4151387 |
0.59 % |
3496162 |
0.52 % |
655225 |
1.87 % |
| q20,qd2,mq40 |
2639553 |
0.38 % |
2569347 |
0.39 % |
70206 |
0.20 % |
| mq40 |
412782 |
0.06 % |
296845 |
0.04 % |
115937 |
0.33 % |
| qd2,mq40 |
18211 |
0.00 % |
14550 |
0.00 % |
3661 |
0.01 % |
| fs60 |
402 |
0.00 % |
0 |
0.00 % |
402 |
0.00 % |
| q20,qd2,fs60 |
402 |
0.00 % |
0 |
0.00 % |
402 |
0.00 % |
| qd2,fs60 |
145 |
0.00 % |
0 |
0.00 % |
145 |
0.00 % |
| fs60,mq40 |
56 |
0.00 % |
0 |
0.00 % |
56 |
0.00 % |
| qd2,fs60,mq40 |
44 |
0.00 % |
0 |
0.00 % |
44 |
0.00 % |
| q20,qd2,fs60,mq40 |
30 |
0.00 % |
0 |
0.00 % |
30 |
0.00 % |
| q20,fs60 |
4 |
0.00 % |
0 |
0.00 % |
4 |
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 |
16809953 |
30.01 % |
| Transition |
G>A |
All |
3655329 |
6.53 % |
| Transition |
T>C |
All |
16807585 |
30.01 % |
| Transition |
C>T |
All |
2485062 |
4.44 % |
| Transversion |
A>C |
All |
1418909 |
2.53 % |
| Transversion |
C>A |
All |
3075535 |
5.49 % |
| Transversion |
T>G |
All |
1636400 |
2.92 % |
| Transversion |
G>T |
All |
2844469 |
5.08 % |
| Transversion |
A>T |
All |
2334522 |
4.17 % |
| Transversion |
T>A |
All |
2643150 |
4.72 % |
| Transversion |
C>G |
All |
1160004 |
2.07 % |
| Transversion |
G>C |
All |
1137622 |
2.03 % |
| |
|
|
|
|
| Transition |
A>G |
Passed |
1956185 |
27.11 % |
| Transition |
G>A |
Passed |
752730 |
10.43 % |
| Transition |
T>C |
Passed |
2611312 |
36.19 % |
| Transition |
C>T |
Passed |
459490 |
6.37 % |
| Transversion |
A>C |
Passed |
179520 |
2.49 % |
| Transversion |
C>A |
Passed |
215042 |
2.98 % |
| Transversion |
T>G |
Passed |
208054 |
2.88 % |
| Transversion |
G>T |
Passed |
144619 |
2.00 % |
| Transversion |
A>T |
Passed |
104184 |
1.44 % |
| Transversion |
T>A |
Passed |
170977 |
2.37 % |
| Transversion |
C>G |
Passed |
202080 |
2.80 % |
| Transversion |
G>C |
Passed |
211593 |
2.93 % |
| |
|
|
|
|
| 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 |
2.45 |
39757929 |
16250611 |
| Passed |
4.02 |
5779717 |
1436069 |
| dbSNPAll |
0 |
0 |
0 |
| dbSNPPassed |
0 |
0 |
0 |