/EXTERNAL CREST/variants/K006458_1_lane_gembs
BACK
SAMPLE K006458_1_lane_gembs
Variant counts
| Type |
Total |
Pass |
% |
| SNPs |
1226096050 |
759846370 |
61.97 % |
| Multiallelic |
0 |
0 |
0.00 % |
VCF Filtering Stats
| Type |
#Sites |
% |
#Non-Variant Sites |
% |
#Variant Sites |
% |
| All |
1226096050 |
100% |
1117993356 |
91.18 % |
108102694 |
8.82 % |
| |
|
|
|
|
|
|
| Passed |
774591183 |
63.18 % |
751533543 |
67.22 % |
23057640 |
2.98 % |
| Filtered |
451504867 |
36.82 % |
366459813 |
32.78 % |
85045054 |
10.98 % |
| |
|
|
|
|
|
|
| q20 |
277040654 |
61.36 % |
258251202 |
70.47 % |
18789452 |
22.09 % |
| q20,qd2 |
88518437 |
19.61 % |
29871000 |
8.15 % |
58647437 |
68.96 % |
| q20,mq40 |
38753311 |
8.58 % |
37065642 |
10.11 % |
1687669 |
1.98 % |
| mq40 |
25489594 |
5.65 % |
23503132 |
6.41 % |
1986462 |
2.34 % |
| qd2 |
14265251 |
3.16 % |
12980736 |
3.54 % |
1284515 |
1.51 % |
| q20,qd2,mq40 |
7245786 |
1.60 % |
4629158 |
1.26 % |
2616628 |
3.08 % |
| qd2,mq40 |
190745 |
0.04 % |
158943 |
0.04 % |
31802 |
0.04 % |
| fs60 |
655 |
0.00 % |
0 |
0.00 % |
655 |
0.00 % |
| fs60,mq40 |
319 |
0.00 % |
0 |
0.00 % |
319 |
0.00 % |
| q20,qd2,fs60 |
72 |
0.00 % |
0 |
0.00 % |
72 |
0.00 % |
| q20,fs60 |
36 |
0.00 % |
0 |
0.00 % |
36 |
0.00 % |
| q20,qd2,fs60,mq40 |
3 |
0.00 % |
0 |
0.00 % |
3 |
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 % |
| 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 |
27392561 |
24.90 % |
| Transition |
G>A |
All |
9841295 |
8.94 % |
| Transition |
T>C |
All |
33565093 |
30.51 % |
| Transition |
C>T |
All |
7028735 |
6.39 % |
| Transversion |
A>C |
All |
2124841 |
1.93 % |
| Transversion |
C>A |
All |
4678925 |
4.25 % |
| Transversion |
T>G |
All |
3391396 |
3.08 % |
| Transversion |
G>T |
All |
4405544 |
4.00 % |
| Transversion |
A>T |
All |
6591965 |
5.99 % |
| Transversion |
T>A |
All |
7054176 |
6.41 % |
| Transversion |
C>G |
All |
2292016 |
2.08 % |
| Transversion |
G>C |
All |
1664767 |
1.51 % |
| |
|
|
|
|
| Transition |
A>G |
Passed |
1940019 |
21.57 % |
| Transition |
G>A |
Passed |
831700 |
9.25 % |
| Transition |
T>C |
Passed |
3079728 |
34.24 % |
| Transition |
C>T |
Passed |
535889 |
5.96 % |
| Transversion |
A>C |
Passed |
271324 |
3.02 % |
| Transversion |
C>A |
Passed |
364355 |
4.05 % |
| Transversion |
T>G |
Passed |
439539 |
4.89 % |
| Transversion |
G>T |
Passed |
202678 |
2.25 % |
| Transversion |
A>T |
Passed |
233768 |
2.60 % |
| Transversion |
T>A |
Passed |
497290 |
5.53 % |
| Transversion |
C>G |
Passed |
344283 |
3.83 % |
| Transversion |
G>C |
Passed |
253566 |
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 |
2.42 |
77827684 |
32203630 |
| Passed |
2.45 |
6387336 |
2606803 |
| dbSNPAll |
0 |
0 |
0 |
| dbSNPPassed |
0 |
0 |
0 |