/EXTERNAL CREST/variants/K006465_1_lane_gembs
BACK
SAMPLE K006465_1_lane_gembs
Variant counts
| Type |
Total |
Pass |
% |
| SNPs |
1203906862 |
839813424 |
69.76 % |
| Multiallelic |
0 |
0 |
0.00 % |
VCF Filtering Stats
| Type |
#Sites |
% |
#Non-Variant Sites |
% |
#Variant Sites |
% |
| All |
1203906862 |
100% |
1124730275 |
93.42 % |
79176587 |
6.58 % |
| |
|
|
|
|
|
|
| Passed |
849260763 |
70.54 % |
833063698 |
74.07 % |
16197065 |
1.91 % |
| Filtered |
354646099 |
29.46 % |
291666577 |
25.93 % |
62979522 |
7.42 % |
| |
|
|
|
|
|
|
| q20 |
208920184 |
58.91 % |
196200423 |
67.27 % |
12719761 |
20.20 % |
| q20,qd2 |
67271038 |
18.97 % |
23027715 |
7.90 % |
44243323 |
70.25 % |
| q20,mq40 |
29834168 |
8.41 % |
28532452 |
9.78 % |
1301716 |
2.07 % |
| mq40 |
26958013 |
7.60 % |
25504948 |
8.74 % |
1453065 |
2.31 % |
| qd2 |
15296767 |
4.31 % |
14119072 |
4.84 % |
1177695 |
1.87 % |
| q20,qd2,mq40 |
6063895 |
1.71 % |
4034201 |
1.38 % |
2029694 |
3.22 % |
| qd2,mq40 |
299598 |
0.08 % |
247766 |
0.08 % |
51832 |
0.08 % |
| fs60 |
1411 |
0.00 % |
0 |
0.00 % |
1411 |
0.00 % |
| fs60,mq40 |
678 |
0.00 % |
0 |
0.00 % |
678 |
0.00 % |
| q20,qd2,fs60 |
204 |
0.00 % |
0 |
0.00 % |
204 |
0.00 % |
| q20,fs60 |
78 |
0.00 % |
0 |
0.00 % |
78 |
0.00 % |
| qd2,fs60 |
24 |
0.00 % |
0 |
0.00 % |
24 |
0.00 % |
| q20,qd2,fs60,mq40 |
18 |
0.00 % |
0 |
0.00 % |
18 |
0.00 % |
| qd2,fs60,mq40 |
16 |
0.00 % |
0 |
0.00 % |
16 |
0.00 % |
| q20,fs60,mq40 |
7 |
0.00 % |
0 |
0.00 % |
7 |
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 |
20854619 |
25.72 % |
| Transition |
G>A |
All |
7035040 |
8.67 % |
| Transition |
T>C |
All |
24461272 |
30.16 % |
| Transition |
C>T |
All |
6743884 |
8.32 % |
| Transversion |
A>C |
All |
1517115 |
1.87 % |
| Transversion |
C>A |
All |
2807320 |
3.46 % |
| Transversion |
T>G |
All |
2594860 |
3.20 % |
| Transversion |
G>T |
All |
2866990 |
3.54 % |
| Transversion |
A>T |
All |
5012014 |
6.18 % |
| Transversion |
T>A |
All |
4735999 |
5.84 % |
| Transversion |
C>G |
All |
1502371 |
1.85 % |
| Transversion |
G>C |
All |
965656 |
1.19 % |
| |
|
|
|
|
| Transition |
A>G |
Passed |
1771103 |
23.46 % |
| Transition |
G>A |
Passed |
812994 |
10.77 % |
| Transition |
T>C |
Passed |
2161677 |
28.64 % |
| Transition |
C>T |
Passed |
607024 |
8.04 % |
| Transversion |
A>C |
Passed |
239054 |
3.17 % |
| Transversion |
C>A |
Passed |
286387 |
3.79 % |
| Transversion |
T>G |
Passed |
413624 |
5.48 % |
| Transversion |
G>T |
Passed |
183022 |
2.42 % |
| Transversion |
A>T |
Passed |
212718 |
2.82 % |
| Transversion |
T>A |
Passed |
378988 |
5.02 % |
| Transversion |
C>G |
Passed |
286884 |
3.80 % |
| Transversion |
G>C |
Passed |
195556 |
2.59 % |
| |
|
|
|
|
| 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 |
2.69 |
59094815 |
22002325 |
| Passed |
2.44 |
5352798 |
2196233 |
| dbSNPAll |
0 |
0 |
0 |
| dbSNPPassed |
0 |
0 |
0 |