/EXTERNAL CREST/variants/K006473_1_lane_gembs
BACK
SAMPLE K006473_1_lane_gembs
Variant counts
| Type |
Total |
Pass |
% |
| SNPs |
1121778088 |
32323125 |
2.88 % |
| Multiallelic |
0 |
0 |
0.00 % |
VCF Filtering Stats
| Type |
#Sites |
% |
#Non-Variant Sites |
% |
#Variant Sites |
% |
| All |
1121778088 |
100% |
1071110425 |
95.48 % |
50667663 |
4.52 % |
| |
|
|
|
|
|
|
| Passed |
52262358 |
4.66 % |
31520889 |
2.94 % |
20741469 |
39.69 % |
| Filtered |
1069515730 |
95.34 % |
1039589536 |
97.06 % |
29926194 |
57.26 % |
| |
|
|
|
|
|
|
| q20 |
905068684 |
84.62 % |
891511876 |
85.76 % |
13556808 |
45.30 % |
| q20,qd2 |
81385328 |
7.61 % |
67632507 |
6.51 % |
13752821 |
45.96 % |
| q20,mq40 |
65233103 |
6.10 % |
64433880 |
6.20 % |
799223 |
2.67 % |
| q20,qd2,mq40 |
15738245 |
1.47 % |
15247620 |
1.47 % |
490625 |
1.64 % |
| mq40 |
2084360 |
0.19 % |
759163 |
0.07 % |
1325197 |
4.43 % |
| qd2,mq40 |
3249 |
0.00 % |
2307 |
0.00 % |
942 |
0.00 % |
| qd2 |
2735 |
0.00 % |
2183 |
0.00 % |
552 |
0.00 % |
| fs60,mq40 |
17 |
0.00 % |
0 |
0.00 % |
17 |
0.00 % |
| fs60 |
6 |
0.00 % |
0 |
0.00 % |
6 |
0.00 % |
| q20,fs60 |
1 |
0.00 % |
0 |
0.00 % |
1 |
0.00 % |
| q20,qd2,fs60 |
1 |
0.00 % |
0 |
0.00 % |
1 |
0.00 % |
| qd2,fs60,mq40 |
1 |
0.00 % |
0 |
0.00 % |
1 |
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 % |
| q20,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 |
8332097 |
15.23 % |
| Transition |
G>A |
All |
3497913 |
6.40 % |
| Transition |
T>C |
All |
8206247 |
15.00 % |
| Transition |
C>T |
All |
2202455 |
4.03 % |
| Transversion |
A>C |
All |
1633573 |
2.99 % |
| Transversion |
C>A |
All |
4883389 |
8.93 % |
| Transversion |
T>G |
All |
3394708 |
6.21 % |
| Transversion |
G>T |
All |
5067381 |
9.27 % |
| Transversion |
A>T |
All |
6941564 |
12.69 % |
| Transversion |
T>A |
All |
6781242 |
12.40 % |
| Transversion |
C>G |
All |
2407763 |
4.40 % |
| Transversion |
G>C |
All |
1343225 |
2.46 % |
| |
|
|
|
|
| Transition |
A>G |
Passed |
137488 |
16.87 % |
| Transition |
G>A |
Passed |
91109 |
11.18 % |
| Transition |
T>C |
Passed |
131686 |
16.16 % |
| Transition |
C>T |
Passed |
56480 |
6.93 % |
| Transversion |
A>C |
Passed |
40787 |
5.00 % |
| Transversion |
C>A |
Passed |
54142 |
6.64 % |
| Transversion |
T>G |
Passed |
70538 |
8.65 % |
| Transversion |
G>T |
Passed |
37987 |
4.66 % |
| Transversion |
A>T |
Passed |
33295 |
4.09 % |
| Transversion |
T>A |
Passed |
60561 |
7.43 % |
| Transversion |
C>G |
Passed |
58650 |
7.20 % |
| Transversion |
G>C |
Passed |
42323 |
5.19 % |
| |
|
|
|
|
| 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 |
0.69 |
22238712 |
32452845 |
| Passed |
1.05 |
416763 |
398283 |
| dbSNPAll |
0 |
0 |
0 |
| dbSNPPassed |
0 |
0 |
0 |