/EXTERNAL CREST/variants/K006442_1_lane_gembs
BACK
SAMPLE K006442_1_lane_gembs
Variant counts
| Type |
Total |
Pass |
% |
| SNPs |
1188219942 |
606700957 |
51.06 % |
| Multiallelic |
0 |
0 |
0.00 % |
VCF Filtering Stats
| Type |
#Sites |
% |
#Non-Variant Sites |
% |
#Variant Sites |
% |
| All |
1188219942 |
100% |
1114649215 |
93.81 % |
73570727 |
6.19 % |
| |
|
|
|
|
|
|
| Passed |
624142302 |
52.53 % |
602431124 |
54.05 % |
21711178 |
3.48 % |
| Filtered |
564077640 |
47.47 % |
512218091 |
45.95 % |
51859549 |
8.31 % |
| |
|
|
|
|
|
|
| q20 |
470922204 |
83.49 % |
454039258 |
88.64 % |
16882946 |
32.56 % |
| q20,qd2 |
61425148 |
10.89 % |
28497647 |
5.56 % |
32927501 |
63.49 % |
| q20,mq40 |
14531296 |
2.58 % |
14092908 |
2.75 % |
438388 |
0.85 % |
| qd2 |
9199893 |
1.63 % |
8619075 |
1.68 % |
580818 |
1.12 % |
| q20,qd2,mq40 |
5268707 |
0.93 % |
4829521 |
0.94 % |
439186 |
0.85 % |
| mq40 |
2672556 |
0.47 % |
2097162 |
0.41 % |
575394 |
1.11 % |
| qd2,mq40 |
54571 |
0.01 % |
42520 |
0.01 % |
12051 |
0.02 % |
| q20,qd2,fs60 |
2310 |
0.00 % |
0 |
0.00 % |
2310 |
0.00 % |
| fs60 |
366 |
0.00 % |
0 |
0.00 % |
366 |
0.00 % |
| fs60,mq40 |
159 |
0.00 % |
0 |
0.00 % |
159 |
0.00 % |
| qd2,fs60 |
157 |
0.00 % |
0 |
0.00 % |
157 |
0.00 % |
| qd2,fs60,mq40 |
152 |
0.00 % |
0 |
0.00 % |
152 |
0.00 % |
| q20,qd2,fs60,mq40 |
105 |
0.00 % |
0 |
0.00 % |
105 |
0.00 % |
| q20,fs60 |
14 |
0.00 % |
0 |
0.00 % |
14 |
0.00 % |
| q20,fs60,mq40 |
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 |
18314463 |
23.92 % |
| Transition |
G>A |
All |
5502204 |
7.19 % |
| Transition |
T>C |
All |
19284571 |
25.19 % |
| Transition |
C>T |
All |
4144909 |
5.41 % |
| Transversion |
A>C |
All |
2204115 |
2.88 % |
| Transversion |
C>A |
All |
3952456 |
5.16 % |
| Transversion |
T>G |
All |
3296291 |
4.31 % |
| Transversion |
G>T |
All |
3574726 |
4.67 % |
| Transversion |
A>T |
All |
5965798 |
7.79 % |
| Transversion |
T>A |
All |
6847392 |
8.94 % |
| Transversion |
C>G |
All |
1965320 |
2.57 % |
| Transversion |
G>C |
All |
1508562 |
1.97 % |
| |
|
|
|
|
| Transition |
A>G |
Passed |
962963 |
20.22 % |
| Transition |
G>A |
Passed |
521911 |
10.96 % |
| Transition |
T>C |
Passed |
1222134 |
25.66 % |
| Transition |
C>T |
Passed |
437823 |
9.19 % |
| Transversion |
A>C |
Passed |
190353 |
4.00 % |
| Transversion |
C>A |
Passed |
205328 |
4.31 % |
| Transversion |
T>G |
Passed |
292735 |
6.15 % |
| Transversion |
G>T |
Passed |
139193 |
2.92 % |
| Transversion |
A>T |
Passed |
138562 |
2.91 % |
| Transversion |
T>A |
Passed |
255336 |
5.36 % |
| Transversion |
C>G |
Passed |
225299 |
4.73 % |
| Transversion |
G>C |
Passed |
171666 |
3.60 % |
| |
|
|
|
|
| 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 |
1.61 |
47246147 |
29314660 |
| Passed |
1.94 |
3144831 |
1618472 |
| dbSNPAll |
0 |
0 |
0 |
| dbSNPPassed |
0 |
0 |
0 |