/EXTERNAL CREST/variants/K006459_1_lane_gembs
BACK
SAMPLE K006459_1_lane_gembs
Variant counts
| Type |
Total |
Pass |
% |
| SNPs |
1228090167 |
626356353 |
51.00 % |
| Multiallelic |
0 |
0 |
0.00 % |
VCF Filtering Stats
| Type |
#Sites |
% |
#Non-Variant Sites |
% |
#Variant Sites |
% |
| All |
1228090167 |
100% |
1099059173 |
89.49 % |
129030994 |
10.51 % |
| |
|
|
|
|
|
|
| Passed |
645850554 |
52.59 % |
618272947 |
56.25 % |
27577607 |
4.27 % |
| Filtered |
582239613 |
47.41 % |
480786226 |
43.75 % |
101453387 |
15.71 % |
| |
|
|
|
|
|
|
| q20 |
393590948 |
67.60 % |
368429471 |
76.63 % |
25161477 |
24.80 % |
| q20,qd2 |
107382646 |
18.44 % |
38683980 |
8.05 % |
68698666 |
67.71 % |
| q20,mq40 |
44788101 |
7.69 % |
42866216 |
8.92 % |
1921885 |
1.89 % |
| mq40 |
18897654 |
3.25 % |
16733115 |
3.48 % |
2164539 |
2.13 % |
| qd2 |
9211790 |
1.58 % |
8504664 |
1.77 % |
707126 |
0.70 % |
| q20,qd2,mq40 |
8267925 |
1.42 % |
5484319 |
1.14 % |
2783606 |
2.74 % |
| qd2,mq40 |
99833 |
0.02 % |
84461 |
0.02 % |
15372 |
0.02 % |
| fs60 |
386 |
0.00 % |
0 |
0.00 % |
386 |
0.00 % |
| fs60,mq40 |
281 |
0.00 % |
0 |
0.00 % |
281 |
0.00 % |
| q20,qd2,fs60 |
25 |
0.00 % |
0 |
0.00 % |
25 |
0.00 % |
| q20,qd2,fs60,mq40 |
9 |
0.00 % |
0 |
0.00 % |
9 |
0.00 % |
| q20,fs60 |
7 |
0.00 % |
0 |
0.00 % |
7 |
0.00 % |
| q20,fs60,mq40 |
4 |
0.00 % |
0 |
0.00 % |
4 |
0.00 % |
| qd2,fs60 |
2 |
0.00 % |
0 |
0.00 % |
2 |
0.00 % |
| qd2,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 |
27792748 |
21.20 % |
| Transition |
G>A |
All |
10244225 |
7.81 % |
| Transition |
T>C |
All |
34629376 |
26.41 % |
| Transition |
C>T |
All |
7427664 |
5.67 % |
| Transversion |
A>C |
All |
2971762 |
2.27 % |
| Transversion |
C>A |
All |
8449879 |
6.44 % |
| Transversion |
T>G |
All |
4580044 |
3.49 % |
| Transversion |
G>T |
All |
8960697 |
6.83 % |
| Transversion |
A>T |
All |
9187957 |
7.01 % |
| Transversion |
T>A |
All |
9413981 |
7.18 % |
| Transversion |
C>G |
All |
4004701 |
3.05 % |
| Transversion |
G>C |
All |
3447938 |
2.63 % |
| |
|
|
|
|
| Transition |
A>G |
Passed |
1638558 |
19.08 % |
| Transition |
G>A |
Passed |
729771 |
8.50 % |
| Transition |
T>C |
Passed |
2534822 |
29.51 % |
| Transition |
C>T |
Passed |
447599 |
5.21 % |
| Transversion |
A>C |
Passed |
287396 |
3.35 % |
| Transversion |
C>A |
Passed |
449702 |
5.24 % |
| Transversion |
T>G |
Passed |
479073 |
5.58 % |
| Transversion |
G>T |
Passed |
260925 |
3.04 % |
| Transversion |
A>T |
Passed |
241315 |
2.81 % |
| Transversion |
T>A |
Passed |
519420 |
6.05 % |
| Transversion |
C>G |
Passed |
534555 |
6.22 % |
| Transversion |
G>C |
Passed |
466385 |
5.43 % |
| |
|
|
|
|
| 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 |
1.57 |
80094013 |
51016959 |
| Passed |
1.65 |
5350750 |
3238771 |
| dbSNPAll |
0 |
0 |
0 |
| dbSNPPassed |
0 |
0 |
0 |