/EXTERNAL KNIH/variants/K006248_1_lane_gembs
BACK
SAMPLE K006248_1_lane_gembs
Variant counts
| Type |
Total |
Pass |
% |
| SNPs |
1193548622 |
337691266 |
28.29 % |
| Multiallelic |
0 |
0 |
0.00 % |
VCF Filtering Stats
| Type |
#Sites |
% |
#Non-Variant Sites |
% |
#Variant Sites |
% |
| All |
1193548622 |
100% |
1100569837 |
92.21 % |
92978785 |
7.79 % |
| |
|
|
|
|
|
|
| Passed |
362983655 |
30.41 % |
329050013 |
29.90 % |
33933642 |
9.35 % |
| Filtered |
830564967 |
69.59 % |
771519824 |
70.10 % |
59045143 |
16.27 % |
| |
|
|
|
|
|
|
| q20 |
742655132 |
89.42 % |
715037367 |
92.68 % |
27617765 |
46.77 % |
| q20,qd2 |
76636711 |
9.23 % |
46003483 |
5.96 % |
30633228 |
51.88 % |
| q20,mq40 |
5918860 |
0.71 % |
5736034 |
0.74 % |
182826 |
0.31 % |
| q20,qd2,mq40 |
3107885 |
0.37 % |
3016247 |
0.39 % |
91638 |
0.16 % |
| qd2 |
1832183 |
0.22 % |
1488231 |
0.19 % |
343952 |
0.58 % |
| mq40 |
401505 |
0.05 % |
229098 |
0.03 % |
172407 |
0.29 % |
| qd2,mq40 |
12360 |
0.00 % |
9364 |
0.00 % |
2996 |
0.01 % |
| fs60 |
151 |
0.00 % |
0 |
0.00 % |
151 |
0.00 % |
| qd2,fs60 |
76 |
0.00 % |
0 |
0.00 % |
76 |
0.00 % |
| q20,qd2,fs60 |
44 |
0.00 % |
0 |
0.00 % |
44 |
0.00 % |
| fs60,mq40 |
24 |
0.00 % |
0 |
0.00 % |
24 |
0.00 % |
| qd2,fs60,mq40 |
23 |
0.00 % |
0 |
0.00 % |
23 |
0.00 % |
| q20,qd2,fs60,mq40 |
13 |
0.00 % |
0 |
0.00 % |
13 |
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 |
30877162 |
31.98 % |
| Transition |
G>A |
All |
4419065 |
4.58 % |
| Transition |
T>C |
All |
30506853 |
31.60 % |
| Transition |
C>T |
All |
2907725 |
3.01 % |
| Transversion |
A>C |
All |
4335797 |
4.49 % |
| Transversion |
C>A |
All |
4006132 |
4.15 % |
| Transversion |
T>G |
All |
4789529 |
4.96 % |
| Transversion |
G>T |
All |
3761693 |
3.90 % |
| Transversion |
A>T |
All |
2390898 |
2.48 % |
| Transversion |
T>A |
All |
2853742 |
2.96 % |
| Transversion |
C>G |
All |
2905397 |
3.01 % |
| Transversion |
G>C |
All |
2786374 |
2.89 % |
| |
|
|
|
|
| Transition |
A>G |
Passed |
2564994 |
28.78 % |
| Transition |
G>A |
Passed |
602303 |
6.76 % |
| Transition |
T>C |
Passed |
3065231 |
34.39 % |
| Transition |
C>T |
Passed |
379546 |
4.26 % |
| Transversion |
A>C |
Passed |
429592 |
4.82 % |
| Transversion |
C>A |
Passed |
284574 |
3.19 % |
| Transversion |
T>G |
Passed |
486998 |
5.46 % |
| Transversion |
G>T |
Passed |
230216 |
2.58 % |
| Transversion |
A>T |
Passed |
111282 |
1.25 % |
| Transversion |
T>A |
Passed |
182416 |
2.05 % |
| Transversion |
C>G |
Passed |
287171 |
3.22 % |
| Transversion |
G>C |
Passed |
289323 |
3.25 % |
| |
|
|
|
|
| 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 |
2.47 |
68710805 |
27829562 |
| Passed |
2.87 |
6612074 |
2301572 |
| dbSNPAll |
0 |
0 |
0 |
| dbSNPPassed |
0 |
0 |
0 |