/EXTERNAL CREST/variants/K006454_1_lane_gembs
BACK
SAMPLE K006454_1_lane_gembs
Variant counts
| Type |
Total |
Pass |
% |
| SNPs |
1229179296 |
618219694 |
50.30 % |
| Multiallelic |
0 |
0 |
0.00 % |
VCF Filtering Stats
| Type |
#Sites |
% |
#Non-Variant Sites |
% |
#Variant Sites |
% |
| All |
1229179296 |
100% |
1113257860 |
90.57 % |
115921436 |
9.43 % |
| |
|
|
|
|
|
|
| Passed |
638584444 |
51.95 % |
611552424 |
54.93 % |
27032020 |
4.23 % |
| Filtered |
590594852 |
48.05 % |
501705436 |
45.07 % |
88889416 |
13.92 % |
| |
|
|
|
|
|
|
| q20 |
426761490 |
72.26 % |
403718534 |
80.47 % |
23042956 |
25.92 % |
| q20,qd2 |
86908783 |
14.72 % |
27226942 |
5.43 % |
59681841 |
67.14 % |
| q20,mq40 |
44394884 |
7.52 % |
42843437 |
8.54 % |
1551447 |
1.75 % |
| mq40 |
19449405 |
3.29 % |
17540370 |
3.50 % |
1909035 |
2.15 % |
| q20,qd2,mq40 |
7320307 |
1.24 % |
5188287 |
1.03 % |
2132020 |
2.40 % |
| qd2 |
5692006 |
0.96 % |
5132377 |
1.02 % |
559629 |
0.63 % |
| qd2,mq40 |
67587 |
0.01 % |
55489 |
0.01 % |
12098 |
0.01 % |
| fs60 |
249 |
0.00 % |
0 |
0.00 % |
249 |
0.00 % |
| fs60,mq40 |
117 |
0.00 % |
0 |
0.00 % |
117 |
0.00 % |
| q20,qd2,fs60 |
20 |
0.00 % |
0 |
0.00 % |
20 |
0.00 % |
| qd2,fs60 |
2 |
0.00 % |
0 |
0.00 % |
2 |
0.00 % |
| q20,fs60 |
1 |
0.00 % |
0 |
0.00 % |
1 |
0.00 % |
| q20,qd2,fs60,mq40 |
1 |
0.00 % |
0 |
0.00 % |
1 |
0.00 % |
| q20,fs60,mq40 |
0 |
0.00 % |
0 |
0.00 % |
0 |
0.00 % |
| qd2,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 |
28664320 |
24.27 % |
| Transition |
G>A |
All |
10055977 |
8.51 % |
| Transition |
T>C |
All |
31608986 |
26.76 % |
| Transition |
C>T |
All |
6492764 |
5.50 % |
| Transversion |
A>C |
All |
2595595 |
2.20 % |
| Transversion |
C>A |
All |
5792314 |
4.90 % |
| Transversion |
T>G |
All |
4335045 |
3.67 % |
| Transversion |
G>T |
All |
5332442 |
4.51 % |
| Transversion |
A>T |
All |
8986334 |
7.61 % |
| Transversion |
T>A |
All |
9541035 |
8.08 % |
| Transversion |
C>G |
All |
2808442 |
2.38 % |
| Transversion |
G>C |
All |
1914424 |
1.62 % |
| |
|
|
|
|
| Transition |
A>G |
Passed |
1592837 |
22.11 % |
| Transition |
G>A |
Passed |
672259 |
9.33 % |
| Transition |
T>C |
Passed |
2120372 |
29.43 % |
| Transition |
C>T |
Passed |
424487 |
5.89 % |
| Transversion |
A>C |
Passed |
252469 |
3.50 % |
| Transversion |
C>A |
Passed |
336978 |
4.68 % |
| Transversion |
T>G |
Passed |
414465 |
5.75 % |
| Transversion |
G>T |
Passed |
182177 |
2.53 % |
| Transversion |
A>T |
Passed |
216296 |
3.00 % |
| Transversion |
T>A |
Passed |
465109 |
6.45 % |
| Transversion |
C>G |
Passed |
308715 |
4.28 % |
| Transversion |
G>C |
Passed |
219324 |
3.04 % |
| |
|
|
|
|
| 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 |
1.86 |
76822047 |
41305631 |
| Passed |
2.01 |
4809955 |
2395533 |
| dbSNPAll |
0 |
0 |
0 |
| dbSNPPassed |
0 |
0 |
0 |