/EXTERNAL CREST/variants/K006474_1_lane_gembs
BACK
SAMPLE K006474_1_lane_gembs
Variant counts
| Type |
Total |
Pass |
% |
| SNPs |
1155446734 |
89797239 |
7.77 % |
| Multiallelic |
0 |
0 |
0.00 % |
VCF Filtering Stats
| Type |
#Sites |
% |
#Non-Variant Sites |
% |
#Variant Sites |
% |
| All |
1155446734 |
100% |
1083005374 |
93.73 % |
72441360 |
6.27 % |
| |
|
|
|
|
|
|
| Passed |
113746581 |
9.84 % |
88840191 |
8.20 % |
24906390 |
21.90 % |
| Filtered |
1041700153 |
90.16 % |
994165183 |
91.80 % |
47534970 |
41.79 % |
| |
|
|
|
|
|
|
| q20 |
896208947 |
86.03 % |
877053305 |
88.22 % |
19155642 |
40.30 % |
| q20,qd2 |
72919624 |
7.00 % |
47693084 |
4.80 % |
25226540 |
53.07 % |
| q20,mq40 |
57260322 |
5.50 % |
56271239 |
5.66 % |
989083 |
2.08 % |
| q20,qd2,mq40 |
12303174 |
1.18 % |
11571051 |
1.16 % |
732123 |
1.54 % |
| mq40 |
2979802 |
0.29 % |
1552043 |
0.16 % |
1427759 |
3.00 % |
| qd2 |
23694 |
0.00 % |
21144 |
0.00 % |
2550 |
0.01 % |
| qd2,mq40 |
4554 |
0.00 % |
3317 |
0.00 % |
1237 |
0.00 % |
| fs60,mq40 |
26 |
0.00 % |
0 |
0.00 % |
26 |
0.00 % |
| fs60 |
7 |
0.00 % |
0 |
0.00 % |
7 |
0.00 % |
| q20,qd2,fs60,mq40 |
2 |
0.00 % |
0 |
0.00 % |
2 |
0.00 % |
| q20,qd2,fs60 |
1 |
0.00 % |
0 |
0.00 % |
1 |
0.00 % |
| q20,fs60 |
0 |
0.00 % |
0 |
0.00 % |
0 |
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 % |
| 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 |
11447151 |
14.90 % |
| Transition |
G>A |
All |
5219805 |
6.79 % |
| Transition |
T>C |
All |
10655646 |
13.87 % |
| Transition |
C>T |
All |
3277722 |
4.27 % |
| Transversion |
A>C |
All |
2417598 |
3.15 % |
| Transversion |
C>A |
All |
7009861 |
9.13 % |
| Transversion |
T>G |
All |
4526235 |
5.89 % |
| Transversion |
G>T |
All |
7370685 |
9.59 % |
| Transversion |
A>T |
All |
10032967 |
13.06 % |
| Transversion |
T>A |
All |
9587345 |
12.48 % |
| Transversion |
C>G |
All |
3326895 |
4.33 % |
| Transversion |
G>C |
All |
1946632 |
2.53 % |
| |
|
|
|
|
| Transition |
A>G |
Passed |
193644 |
18.89 % |
| Transition |
G>A |
Passed |
81624 |
7.96 % |
| Transition |
T>C |
Passed |
169299 |
16.52 % |
| Transition |
C>T |
Passed |
31681 |
3.09 % |
| Transversion |
A>C |
Passed |
50422 |
4.92 % |
| Transversion |
C>A |
Passed |
77576 |
7.57 % |
| Transversion |
T>G |
Passed |
108840 |
10.62 % |
| Transversion |
G>T |
Passed |
39757 |
3.88 % |
| Transversion |
A>T |
Passed |
46632 |
4.55 % |
| Transversion |
T>A |
Passed |
100870 |
9.84 % |
| Transversion |
C>G |
Passed |
81828 |
7.98 % |
| Transversion |
G>C |
Passed |
42812 |
4.18 % |
| |
|
|
|
|
| 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 |
0.66 |
30600324 |
46218218 |
| Passed |
0.87 |
476248 |
548737 |
| dbSNPAll |
0 |
0 |
0 |
| dbSNPPassed |
0 |
0 |
0 |