/EXTERNAL DEEP/variants/K006096_K006097_K006098_K006099_4_lane_gembs
BACK
SAMPLE K006096_K006097_K006098_K006099_4_lane_gembs
Variant counts
| Type |
Total |
Pass |
% |
| SNPs |
1176906659 |
767308206 |
65.20 % |
| Multiallelic |
0 |
0 |
0.00 % |
VCF Filtering Stats
| Type |
#Sites |
% |
#Non-Variant Sites |
% |
#Variant Sites |
% |
| All |
1176906659 |
100% |
1134341730 |
96.38 % |
42564929 |
3.62 % |
| |
|
|
|
|
|
|
| Passed |
774153205 |
65.78 % |
760688719 |
67.06 % |
13464486 |
1.74 % |
| Filtered |
402753454 |
34.22 % |
373653011 |
32.94 % |
29100443 |
3.76 % |
| |
|
|
|
|
|
|
| q20 |
349549233 |
86.79 % |
340670550 |
91.17 % |
8878683 |
30.51 % |
| q20,qd2 |
31501132 |
7.82 % |
12687088 |
3.40 % |
18814044 |
64.65 % |
| q20,mq40 |
9985632 |
2.48 % |
9753163 |
2.61 % |
232469 |
0.80 % |
| qd2 |
7127422 |
1.77 % |
6441853 |
1.72 % |
685569 |
2.36 % |
| q20,qd2,mq40 |
3019871 |
0.75 % |
2817876 |
0.75 % |
201995 |
0.69 % |
| mq40 |
1514061 |
0.38 % |
1238647 |
0.33 % |
275414 |
0.95 % |
| qd2,mq40 |
53350 |
0.01 % |
43834 |
0.01 % |
9516 |
0.03 % |
| qd2,fs60,mq40 |
884 |
0.00 % |
0 |
0.00 % |
884 |
0.00 % |
| qd2,fs60 |
611 |
0.00 % |
0 |
0.00 % |
611 |
0.00 % |
| q20,qd2,fs60 |
384 |
0.00 % |
0 |
0.00 % |
384 |
0.00 % |
| fs60 |
371 |
0.00 % |
0 |
0.00 % |
371 |
0.00 % |
| fs60,mq40 |
325 |
0.00 % |
0 |
0.00 % |
325 |
0.00 % |
| q20,qd2,fs60,mq40 |
176 |
0.00 % |
0 |
0.00 % |
176 |
0.00 % |
| q20,fs60 |
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 |
14011786 |
31.88 % |
| Transition |
G>A |
All |
3226975 |
7.34 % |
| Transition |
T>C |
All |
16714794 |
38.03 % |
| Transition |
C>T |
All |
2453762 |
5.58 % |
| Transversion |
A>C |
All |
638237 |
1.45 % |
| Transversion |
C>A |
All |
1562488 |
3.56 % |
| Transversion |
T>G |
All |
773766 |
1.76 % |
| Transversion |
G>T |
All |
1424922 |
3.24 % |
| Transversion |
A>T |
All |
1008052 |
2.29 % |
| Transversion |
T>A |
All |
1132380 |
2.58 % |
| Transversion |
C>G |
All |
511515 |
1.16 % |
| Transversion |
G>C |
All |
490488 |
1.12 % |
| |
|
|
|
|
| Transition |
A>G |
Passed |
1445155 |
20.73 % |
| Transition |
G>A |
Passed |
762067 |
10.93 % |
| Transition |
T>C |
Passed |
2492586 |
35.76 % |
| Transition |
C>T |
Passed |
637267 |
9.14 % |
| Transversion |
A>C |
Passed |
182814 |
2.62 % |
| Transversion |
C>A |
Passed |
278573 |
4.00 % |
| Transversion |
T>G |
Passed |
205464 |
2.95 % |
| Transversion |
G>T |
Passed |
236095 |
3.39 % |
| Transversion |
A>T |
Passed |
151808 |
2.18 % |
| Transversion |
T>A |
Passed |
189167 |
2.71 % |
| Transversion |
C>G |
Passed |
197799 |
2.84 % |
| Transversion |
G>C |
Passed |
192479 |
2.76 % |
| |
|
|
|
|
| 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 |
4.83 |
36407317 |
7541848 |
| Passed |
3.27 |
5337075 |
1634199 |
| dbSNPAll |
0 |
0 |
0 |
| dbSNPPassed |
0 |
0 |
0 |