/EXTERNAL CREST/variants/K006441_1_lane_gembs
BACK
SAMPLE K006441_1_lane_gembs
Variant counts
| Type |
Total |
Pass |
% |
| SNPs |
1189227981 |
539218252 |
45.34 % |
| Multiallelic |
0 |
0 |
0.00 % |
VCF Filtering Stats
| Type |
#Sites |
% |
#Non-Variant Sites |
% |
#Variant Sites |
% |
| All |
1189227981 |
100% |
1111455270 |
93.46 % |
77772711 |
6.54 % |
| |
|
|
|
|
|
|
| Passed |
558384031 |
46.95 % |
535125289 |
48.15 % |
23258742 |
4.17 % |
| Filtered |
630843950 |
53.05 % |
576329981 |
51.85 % |
54513969 |
9.76 % |
| |
|
|
|
|
|
|
| q20 |
527923921 |
83.69 % |
509901249 |
88.47 % |
18022672 |
33.06 % |
| q20,qd2 |
67693058 |
10.73 % |
33347314 |
5.79 % |
34345744 |
63.00 % |
| q20,mq40 |
16899967 |
2.68 % |
16423498 |
2.85 % |
476469 |
0.87 % |
| qd2 |
9309887 |
1.48 % |
8801066 |
1.53 % |
508821 |
0.93 % |
| q20,qd2,mq40 |
6237219 |
0.99 % |
5758226 |
1.00 % |
478993 |
0.88 % |
| mq40 |
2731212 |
0.43 % |
2061188 |
0.36 % |
670024 |
1.23 % |
| qd2,mq40 |
46658 |
0.01 % |
37440 |
0.01 % |
9218 |
0.02 % |
| q20,qd2,fs60 |
1154 |
0.00 % |
0 |
0.00 % |
1154 |
0.00 % |
| fs60 |
372 |
0.00 % |
0 |
0.00 % |
372 |
0.00 % |
| qd2,fs60 |
172 |
0.00 % |
0 |
0.00 % |
172 |
0.00 % |
| qd2,fs60,mq40 |
126 |
0.00 % |
0 |
0.00 % |
126 |
0.00 % |
| fs60,mq40 |
124 |
0.00 % |
0 |
0.00 % |
124 |
0.00 % |
| q20,qd2,fs60,mq40 |
72 |
0.00 % |
0 |
0.00 % |
72 |
0.00 % |
| q20,fs60 |
8 |
0.00 % |
0 |
0.00 % |
8 |
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 |
16691301 |
20.57 % |
| Transition |
G>A |
All |
6245314 |
7.70 % |
| Transition |
T>C |
All |
19126624 |
23.57 % |
| Transition |
C>T |
All |
4868649 |
6.00 % |
| Transversion |
A>C |
All |
2678661 |
3.30 % |
| Transversion |
C>A |
All |
4708086 |
5.80 % |
| Transversion |
T>G |
All |
3473033 |
4.28 % |
| Transversion |
G>T |
All |
4453973 |
5.49 % |
| Transversion |
A>T |
All |
7130103 |
8.79 % |
| Transversion |
T>A |
All |
7804432 |
9.62 % |
| Transversion |
C>G |
All |
2152116 |
2.65 % |
| Transversion |
G>C |
All |
1827333 |
2.25 % |
| |
|
|
|
|
| Transition |
A>G |
Passed |
813562 |
17.81 % |
| Transition |
G>A |
Passed |
506109 |
11.08 % |
| Transition |
T>C |
Passed |
1166685 |
25.53 % |
| Transition |
C>T |
Passed |
417497 |
9.14 % |
| Transversion |
A>C |
Passed |
212316 |
4.65 % |
| Transversion |
C>A |
Passed |
209815 |
4.59 % |
| Transversion |
T>G |
Passed |
275460 |
6.03 % |
| Transversion |
G>T |
Passed |
153668 |
3.36 % |
| Transversion |
A>T |
Passed |
154974 |
3.39 % |
| Transversion |
T>A |
Passed |
252877 |
5.53 % |
| Transversion |
C>G |
Passed |
221254 |
4.84 % |
| Transversion |
G>C |
Passed |
184836 |
4.05 % |
| |
|
|
|
|
| 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 |
1.37 |
46931888 |
34227737 |
| Passed |
1.74 |
2903853 |
1665200 |
| dbSNPAll |
0 |
0 |
0 |
| dbSNPPassed |
0 |
0 |
0 |