/EXTERNAL KNIH/variants/K006229_1_lane_gembs
BACK
SAMPLE K006229_1_lane_gembs
Variant counts
| Type |
Total |
Pass |
% |
| SNPs |
1156658895 |
1011576309 |
87.46 % |
| Multiallelic |
0 |
0 |
0.00 % |
VCF Filtering Stats
| Type |
#Sites |
% |
#Non-Variant Sites |
% |
#Variant Sites |
% |
| All |
1156658895 |
100% |
1140983049 |
98.64 % |
15675846 |
1.36 % |
| |
|
|
|
|
|
|
| Passed |
1013596794 |
87.63 % |
1009145101 |
88.45 % |
4451693 |
0.44 % |
| Filtered |
143062101 |
12.37 % |
131837948 |
11.55 % |
11224153 |
1.11 % |
| |
|
|
|
|
|
|
| q20 |
102575593 |
71.70 % |
101205497 |
76.77 % |
1370096 |
12.21 % |
| q20,mq40 |
14998167 |
10.48 % |
14831704 |
11.25 % |
166463 |
1.48 % |
| q20,qd2 |
11793495 |
8.24 % |
3087388 |
2.34 % |
8706107 |
77.57 % |
| mq40 |
8182123 |
5.72 % |
7854832 |
5.96 % |
327291 |
2.92 % |
| q20,qd2,mq40 |
3008790 |
2.10 % |
2730594 |
2.07 % |
278196 |
2.48 % |
| qd2 |
2407097 |
1.68 % |
2051401 |
1.56 % |
355696 |
3.17 % |
| qd2,mq40 |
91336 |
0.06 % |
76532 |
0.06 % |
14804 |
0.13 % |
| qd2,fs60,mq40 |
1684 |
0.00 % |
0 |
0.00 % |
1684 |
0.02 % |
| fs60 |
1152 |
0.00 % |
0 |
0.00 % |
1152 |
0.01 % |
| q20,qd2,fs60 |
881 |
0.00 % |
0 |
0.00 % |
881 |
0.01 % |
| qd2,fs60 |
855 |
0.00 % |
0 |
0.00 % |
855 |
0.01 % |
| fs60,mq40 |
680 |
0.00 % |
0 |
0.00 % |
680 |
0.01 % |
| q20,qd2,fs60,mq40 |
240 |
0.00 % |
0 |
0.00 % |
240 |
0.00 % |
| q20,fs60,mq40 |
6 |
0.00 % |
0 |
0.00 % |
6 |
0.00 % |
| q20,fs60 |
2 |
0.00 % |
0 |
0.00 % |
2 |
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 |
6611523 |
37.68 % |
| Transition |
G>A |
All |
1025968 |
5.85 % |
| Transition |
T>C |
All |
6577189 |
37.49 % |
| Transition |
C>T |
All |
1025887 |
5.85 % |
| Transversion |
A>C |
All |
237579 |
1.35 % |
| Transversion |
C>A |
All |
385693 |
2.20 % |
| Transversion |
T>G |
All |
241237 |
1.37 % |
| Transversion |
G>T |
All |
382509 |
2.18 % |
| Transversion |
A>T |
All |
316701 |
1.81 % |
| Transversion |
T>A |
All |
307693 |
1.75 % |
| Transversion |
C>G |
All |
217612 |
1.24 % |
| Transversion |
G>C |
All |
215890 |
1.23 % |
| |
|
|
|
|
| Transition |
A>G |
Passed |
719750 |
19.55 % |
| Transition |
G>A |
Passed |
561469 |
15.25 % |
| Transition |
T>C |
Passed |
718207 |
19.51 % |
| Transition |
C>T |
Passed |
564259 |
15.33 % |
| Transversion |
A>C |
Passed |
144634 |
3.93 % |
| Transversion |
C>A |
Passed |
144057 |
3.91 % |
| Transversion |
T>G |
Passed |
144946 |
3.94 % |
| Transversion |
G>T |
Passed |
144531 |
3.93 % |
| Transversion |
A>T |
Passed |
123925 |
3.37 % |
| Transversion |
T>A |
Passed |
123899 |
3.37 % |
| Transversion |
C>G |
Passed |
145867 |
3.96 % |
| Transversion |
G>C |
Passed |
145658 |
3.96 % |
| |
|
|
|
|
| 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 |
6.61 |
15240567 |
2304914 |
| Passed |
2.29 |
2563685 |
1117517 |
| dbSNPAll |
0 |
0 |
0 |
| dbSNPPassed |
0 |
0 |
0 |