/EXTERNAL CREST/variants/K006452_1_lane_gembs
BACK
SAMPLE K006452_1_lane_gembs
Variant counts
| Type |
Total |
Pass |
% |
| SNPs |
1226108417 |
770674068 |
62.86 % |
| Multiallelic |
0 |
0 |
0.00 % |
VCF Filtering Stats
| Type |
#Sites |
% |
#Non-Variant Sites |
% |
#Variant Sites |
% |
| All |
1226108417 |
100% |
1119780217 |
91.33 % |
106328200 |
8.67 % |
| |
|
|
|
|
|
|
| Passed |
784802672 |
64.01 % |
762366975 |
68.08 % |
22435697 |
2.86 % |
| Filtered |
441305745 |
35.99 % |
357413242 |
31.92 % |
83892503 |
10.69 % |
| |
|
|
|
|
|
|
| q20 |
269329379 |
61.03 % |
250632636 |
70.12 % |
18696743 |
22.29 % |
| q20,qd2 |
86791471 |
19.67 % |
29200924 |
8.17 % |
57590547 |
68.65 % |
| q20,mq40 |
37572434 |
8.51 % |
35880912 |
10.04 % |
1691522 |
2.02 % |
| mq40 |
26667248 |
6.04 % |
24713126 |
6.91 % |
1954122 |
2.33 % |
| qd2 |
13506002 |
3.06 % |
12219716 |
3.42 % |
1286286 |
1.53 % |
| q20,qd2,mq40 |
7229935 |
1.64 % |
4596109 |
1.29 % |
2633826 |
3.14 % |
| qd2,mq40 |
207929 |
0.05 % |
169819 |
0.05 % |
38110 |
0.05 % |
| fs60 |
767 |
0.00 % |
0 |
0.00 % |
767 |
0.00 % |
| fs60,mq40 |
468 |
0.00 % |
0 |
0.00 % |
468 |
0.00 % |
| q20,qd2,fs60 |
59 |
0.00 % |
0 |
0.00 % |
59 |
0.00 % |
| q20,fs60 |
30 |
0.00 % |
0 |
0.00 % |
30 |
0.00 % |
| q20,qd2,fs60,mq40 |
10 |
0.00 % |
0 |
0.00 % |
10 |
0.00 % |
| qd2,fs60,mq40 |
7 |
0.00 % |
0 |
0.00 % |
7 |
0.00 % |
| qd2,fs60 |
5 |
0.00 % |
0 |
0.00 % |
5 |
0.00 % |
| q20,fs60,mq40 |
1 |
0.00 % |
0 |
0.00 % |
1 |
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 |
27088221 |
25.02 % |
| Transition |
G>A |
All |
9539227 |
8.81 % |
| Transition |
T>C |
All |
33943770 |
31.35 % |
| Transition |
C>T |
All |
6936360 |
6.41 % |
| Transversion |
A>C |
All |
2121247 |
1.96 % |
| Transversion |
C>A |
All |
4332405 |
4.00 % |
| Transversion |
T>G |
All |
3342859 |
3.09 % |
| Transversion |
G>T |
All |
4071387 |
3.76 % |
| Transversion |
A>T |
All |
6357280 |
5.87 % |
| Transversion |
T>A |
All |
6785004 |
6.27 % |
| Transversion |
C>G |
All |
2165353 |
2.00 % |
| Transversion |
G>C |
All |
1583077 |
1.46 % |
| |
|
|
|
|
| Transition |
A>G |
Passed |
1938359 |
21.52 % |
| Transition |
G>A |
Passed |
827264 |
9.18 % |
| Transition |
T>C |
Passed |
3170924 |
35.21 % |
| Transition |
C>T |
Passed |
534800 |
5.94 % |
| Transversion |
A>C |
Passed |
270231 |
3.00 % |
| Transversion |
C>A |
Passed |
350906 |
3.90 % |
| Transversion |
T>G |
Passed |
433335 |
4.81 % |
| Transversion |
G>T |
Passed |
197328 |
2.19 % |
| Transversion |
A>T |
Passed |
229182 |
2.54 % |
| Transversion |
T>A |
Passed |
481051 |
5.34 % |
| Transversion |
C>G |
Passed |
328978 |
3.65 % |
| Transversion |
G>C |
Passed |
244537 |
2.71 % |
| |
|
|
|
|
| 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 |
2.52 |
77507578 |
30758612 |
| Passed |
2.55 |
6471347 |
2535548 |
| dbSNPAll |
0 |
0 |
0 |
| dbSNPPassed |
0 |
0 |
0 |