/EXTERNAL CREST/variants/K006477_1_lane_gembs
BACK
SAMPLE K006477_1_lane_gembs
Variant counts
| Type |
Total |
Pass |
% |
| SNPs |
1133823141 |
51680338 |
4.56 % |
| Multiallelic |
0 |
0 |
0.00 % |
VCF Filtering Stats
| Type |
#Sites |
% |
#Non-Variant Sites |
% |
#Variant Sites |
% |
| All |
1133823141 |
100% |
1077514728 |
95.03 % |
56308413 |
4.97 % |
| |
|
|
|
|
|
|
| Passed |
72085623 |
6.36 % |
50698703 |
4.71 % |
21386920 |
29.67 % |
| Filtered |
1061737518 |
93.64 % |
1026816025 |
95.29 % |
34921493 |
48.44 % |
| |
|
|
|
|
|
|
| q20 |
904780654 |
85.22 % |
889683344 |
86.64 % |
15097310 |
43.23 % |
| q20,qd2 |
75487024 |
7.11 % |
58445048 |
5.69 % |
17041976 |
48.80 % |
| q20,mq40 |
64446491 |
6.07 % |
63583584 |
6.19 % |
862907 |
2.47 % |
| q20,qd2,mq40 |
14564221 |
1.37 % |
13986838 |
1.36 % |
577383 |
1.65 % |
| mq40 |
2449952 |
0.23 % |
1109863 |
0.11 % |
1340089 |
3.84 % |
| qd2 |
5751 |
0.00 % |
4893 |
0.00 % |
858 |
0.00 % |
| qd2,mq40 |
3401 |
0.00 % |
2455 |
0.00 % |
946 |
0.00 % |
| fs60,mq40 |
22 |
0.00 % |
0 |
0.00 % |
22 |
0.00 % |
| q20,qd2,fs60 |
1 |
0.00 % |
0 |
0.00 % |
1 |
0.00 % |
| q20,qd2,fs60,mq40 |
1 |
0.00 % |
0 |
0.00 % |
1 |
0.00 % |
| fs60 |
0 |
0.00 % |
0 |
0.00 % |
0 |
0.00 % |
| q20,fs60 |
0 |
0.00 % |
0 |
0.00 % |
0 |
0.00 % |
| qd2,fs60 |
0 |
0.00 % |
0 |
0.00 % |
0 |
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 |
9089001 |
15.10 % |
| Transition |
G>A |
All |
3931313 |
6.53 % |
| Transition |
T>C |
All |
8865270 |
14.73 % |
| Transition |
C>T |
All |
2515965 |
4.18 % |
| Transversion |
A>C |
All |
1820696 |
3.03 % |
| Transversion |
C>A |
All |
5425695 |
9.02 % |
| Transversion |
T>G |
All |
3644759 |
6.06 % |
| Transversion |
G>T |
All |
5605548 |
9.32 % |
| Transversion |
A>T |
All |
7678854 |
12.76 % |
| Transversion |
T>A |
All |
7514256 |
12.49 % |
| Transversion |
C>G |
All |
2605264 |
4.33 % |
| Transversion |
G>C |
All |
1479841 |
2.46 % |
| |
|
|
|
|
| Transition |
A>G |
Passed |
170195 |
16.93 % |
| Transition |
G>A |
Passed |
112677 |
11.21 % |
| Transition |
T>C |
Passed |
161796 |
16.09 % |
| Transition |
C>T |
Passed |
68381 |
6.80 % |
| Transversion |
A>C |
Passed |
48892 |
4.86 % |
| Transversion |
C>A |
Passed |
68734 |
6.84 % |
| Transversion |
T>G |
Passed |
86702 |
8.62 % |
| Transversion |
G>T |
Passed |
45962 |
4.57 % |
| Transversion |
A>T |
Passed |
41703 |
4.15 % |
| Transversion |
T>A |
Passed |
78674 |
7.83 % |
| Transversion |
C>G |
Passed |
72209 |
7.18 % |
| Transversion |
G>C |
Passed |
49341 |
4.91 % |
| |
|
|
|
|
| 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 |
0.68 |
24401549 |
35774913 |
| Passed |
1.04 |
513049 |
492217 |
| dbSNPAll |
0 |
0 |
0 |
| dbSNPPassed |
0 |
0 |
0 |