/EXTERNAL CREST/variants/K006457_1_lane_gembs
BACK
SAMPLE K006457_1_lane_gembs
Variant counts
| Type |
Total |
Pass |
% |
| SNPs |
1225900843 |
772447989 |
63.01 % |
| Multiallelic |
0 |
0 |
0.00 % |
VCF Filtering Stats
| Type |
#Sites |
% |
#Non-Variant Sites |
% |
#Variant Sites |
% |
| All |
1225900843 |
100% |
1118686177 |
91.25 % |
107214666 |
8.75 % |
| |
|
|
|
|
|
|
| Passed |
786736143 |
64.18 % |
763931020 |
68.29 % |
22805123 |
2.90 % |
| Filtered |
439164700 |
35.82 % |
354755157 |
31.71 % |
84409543 |
10.73 % |
| |
|
|
|
|
|
|
| q20 |
263685623 |
60.04 % |
245240002 |
69.13 % |
18445621 |
21.85 % |
| q20,qd2 |
88244626 |
20.09 % |
30069320 |
8.48 % |
58175306 |
68.92 % |
| q20,mq40 |
38092035 |
8.67 % |
36396602 |
10.26 % |
1695433 |
2.01 % |
| mq40 |
26126731 |
5.95 % |
24117231 |
6.80 % |
2009500 |
2.38 % |
| qd2 |
15502306 |
3.53 % |
14120964 |
3.98 % |
1381342 |
1.64 % |
| q20,qd2,mq40 |
7303716 |
1.66 % |
4637612 |
1.31 % |
2666104 |
3.16 % |
| qd2,mq40 |
208427 |
0.05 % |
173426 |
0.05 % |
35001 |
0.04 % |
| fs60 |
717 |
0.00 % |
0 |
0.00 % |
717 |
0.00 % |
| fs60,mq40 |
378 |
0.00 % |
0 |
0.00 % |
378 |
0.00 % |
| q20,qd2,fs60 |
88 |
0.00 % |
0 |
0.00 % |
88 |
0.00 % |
| q20,fs60 |
44 |
0.00 % |
0 |
0.00 % |
44 |
0.00 % |
| qd2,fs60,mq40 |
3 |
0.00 % |
0 |
0.00 % |
3 |
0.00 % |
| q20,qd2,fs60,mq40 |
3 |
0.00 % |
0 |
0.00 % |
3 |
0.00 % |
| q20,fs60,mq40 |
2 |
0.00 % |
0 |
0.00 % |
2 |
0.00 % |
| qd2,fs60 |
1 |
0.00 % |
0 |
0.00 % |
1 |
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 |
27076127 |
24.81 % |
| Transition |
G>A |
All |
9624094 |
8.82 % |
| Transition |
T>C |
All |
33906100 |
31.07 % |
| Transition |
C>T |
All |
7061292 |
6.47 % |
| Transversion |
A>C |
All |
2096592 |
1.92 % |
| Transversion |
C>A |
All |
4589955 |
4.21 % |
| Transversion |
T>G |
All |
3313071 |
3.04 % |
| Transversion |
G>T |
All |
4355367 |
3.99 % |
| Transversion |
A>T |
All |
6367968 |
5.84 % |
| Transversion |
T>A |
All |
6814210 |
6.24 % |
| Transversion |
C>G |
All |
2247466 |
2.06 % |
| Transversion |
G>C |
All |
1665844 |
1.53 % |
| |
|
|
|
|
| Transition |
A>G |
Passed |
1977578 |
21.48 % |
| Transition |
G>A |
Passed |
839329 |
9.12 % |
| Transition |
T>C |
Passed |
3230013 |
35.08 % |
| Transition |
C>T |
Passed |
547279 |
5.94 % |
| Transversion |
A>C |
Passed |
272352 |
2.96 % |
| Transversion |
C>A |
Passed |
365014 |
3.96 % |
| Transversion |
T>G |
Passed |
436821 |
4.74 % |
| Transversion |
G>T |
Passed |
205266 |
2.23 % |
| Transversion |
A>T |
Passed |
233081 |
2.53 % |
| Transversion |
T>A |
Passed |
492516 |
5.35 % |
| Transversion |
C>G |
Passed |
347417 |
3.77 % |
| Transversion |
G>C |
Passed |
260066 |
2.82 % |
| |
|
|
|
|
| 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 |
2.47 |
77667613 |
31450473 |
| Passed |
2.52 |
6594199 |
2612533 |
| dbSNPAll |
0 |
0 |
0 |
| dbSNPPassed |
0 |
0 |
0 |