/EXTERNAL CREST/variants/K006433_1_lane_gembs
BACK
SAMPLE K006433_1_lane_gembs
Variant counts
| Type |
Total |
Pass |
% |
| SNPs |
1214867182 |
744001985 |
61.24 % |
| Multiallelic |
0 |
0 |
0.00 % |
VCF Filtering Stats
| Type |
#Sites |
% |
#Non-Variant Sites |
% |
#Variant Sites |
% |
| All |
1214867182 |
100% |
1124288628 |
92.54 % |
90578554 |
7.46 % |
| |
|
|
|
|
|
|
| Passed |
756137036 |
62.24 % |
736845196 |
65.54 % |
19291840 |
2.55 % |
| Filtered |
458730146 |
37.76 % |
387443432 |
34.46 % |
71286714 |
9.43 % |
| |
|
|
|
|
|
|
| q20 |
299284719 |
65.24 % |
281587626 |
72.68 % |
17697093 |
24.83 % |
| q20,qd2 |
70011645 |
15.26 % |
23488124 |
6.06 % |
46523521 |
65.26 % |
| q20,mq40 |
42271812 |
9.21 % |
40570005 |
10.47 % |
1701807 |
2.39 % |
| mq40 |
28945672 |
6.31 % |
26993794 |
6.97 % |
1951878 |
2.74 % |
| qd2 |
10746198 |
2.34 % |
9859749 |
2.54 % |
886449 |
1.24 % |
| q20,qd2,mq40 |
7260430 |
1.58 % |
4774515 |
1.23 % |
2485915 |
3.49 % |
| qd2,mq40 |
208599 |
0.05 % |
169619 |
0.04 % |
38980 |
0.05 % |
| fs60 |
594 |
0.00 % |
0 |
0.00 % |
594 |
0.00 % |
| fs60,mq40 |
387 |
0.00 % |
0 |
0.00 % |
387 |
0.00 % |
| q20,qd2,fs60 |
42 |
0.00 % |
0 |
0.00 % |
42 |
0.00 % |
| q20,fs60 |
23 |
0.00 % |
0 |
0.00 % |
23 |
0.00 % |
| qd2,fs60 |
12 |
0.00 % |
0 |
0.00 % |
12 |
0.00 % |
| q20,qd2,fs60,mq40 |
10 |
0.00 % |
0 |
0.00 % |
10 |
0.00 % |
| qd2,fs60,mq40 |
3 |
0.00 % |
0 |
0.00 % |
3 |
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 |
22631629 |
24.47 % |
| Transition |
G>A |
All |
8025524 |
8.68 % |
| Transition |
T>C |
All |
29486971 |
31.88 % |
| Transition |
C>T |
All |
6095403 |
6.59 % |
| Transversion |
A>C |
All |
1970544 |
2.13 % |
| Transversion |
C>A |
All |
3443050 |
3.72 % |
| Transversion |
T>G |
All |
3304220 |
3.57 % |
| Transversion |
G>T |
All |
3077030 |
3.33 % |
| Transversion |
A>T |
All |
5270361 |
5.70 % |
| Transversion |
T>A |
All |
5779136 |
6.25 % |
| Transversion |
C>G |
All |
2021672 |
2.19 % |
| Transversion |
G>C |
All |
1379783 |
1.49 % |
| |
|
|
|
|
| Transition |
A>G |
Passed |
1605891 |
20.52 % |
| Transition |
G>A |
Passed |
725726 |
9.27 % |
| Transition |
T>C |
Passed |
2840680 |
36.30 % |
| Transition |
C>T |
Passed |
471849 |
6.03 % |
| Transversion |
A>C |
Passed |
230201 |
2.94 % |
| Transversion |
C>A |
Passed |
292061 |
3.73 % |
| Transversion |
T>G |
Passed |
417922 |
5.34 % |
| Transversion |
G>T |
Passed |
159649 |
2.04 % |
| Transversion |
A>T |
Passed |
180141 |
2.30 % |
| Transversion |
T>A |
Passed |
401955 |
5.14 % |
| Transversion |
C>G |
Passed |
300520 |
3.84 % |
| Transversion |
G>C |
Passed |
199864 |
2.55 % |
| |
|
|
|
|
| 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 |
66239527 |
26245796 |
| Passed |
2.59 |
5644146 |
2182313 |
| dbSNPAll |
0 |
0 |
0 |
| dbSNPPassed |
0 |
0 |
0 |