/EXTERNAL DEEP/variants/K009046_K009047_K009048_3_lane_gembs
BACK
SAMPLE K009046_K009047_K009048_3_lane_gembs
Variant counts
| Type |
Total |
Pass |
% |
| SNPs |
1176007365 |
768865373 |
65.38 % |
| Multiallelic |
0 |
0 |
0.00 % |
VCF Filtering Stats
| Type |
#Sites |
% |
#Non-Variant Sites |
% |
#Variant Sites |
% |
| All |
1176007365 |
100% |
1139380913 |
96.89 % |
36626452 |
3.11 % |
| |
|
|
|
|
|
|
| Passed |
774453126 |
65.85 % |
764318547 |
67.08 % |
10134579 |
1.31 % |
| Filtered |
401554239 |
34.15 % |
375062366 |
32.92 % |
26491873 |
3.42 % |
| |
|
|
|
|
|
|
| q20 |
355712437 |
88.58 % |
348211485 |
92.84 % |
7500952 |
28.31 % |
| q20,qd2 |
29138354 |
7.26 % |
11019519 |
2.94 % |
18118835 |
68.39 % |
| q20,mq40 |
8622736 |
2.15 % |
8486663 |
2.26 % |
136073 |
0.51 % |
| qd2 |
4348061 |
1.08 % |
3937623 |
1.05 % |
410438 |
1.55 % |
| q20,qd2,mq40 |
2778271 |
0.69 % |
2660521 |
0.71 % |
117750 |
0.44 % |
| mq40 |
925326 |
0.23 % |
724602 |
0.19 % |
200724 |
0.76 % |
| qd2,mq40 |
27745 |
0.01 % |
21953 |
0.01 % |
5792 |
0.02 % |
| qd2,fs60,mq40 |
481 |
0.00 % |
0 |
0.00 % |
481 |
0.00 % |
| qd2,fs60 |
243 |
0.00 % |
0 |
0.00 % |
243 |
0.00 % |
| fs60 |
238 |
0.00 % |
0 |
0.00 % |
238 |
0.00 % |
| fs60,mq40 |
188 |
0.00 % |
0 |
0.00 % |
188 |
0.00 % |
| q20,qd2,fs60 |
95 |
0.00 % |
0 |
0.00 % |
95 |
0.00 % |
| q20,qd2,fs60,mq40 |
64 |
0.00 % |
0 |
0.00 % |
64 |
0.00 % |
| q20,fs60 |
0 |
0.00 % |
0 |
0.00 % |
0 |
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 |
12417065 |
32.23 % |
| Transition |
G>A |
All |
3078321 |
7.99 % |
| Transition |
T>C |
All |
14525822 |
37.70 % |
| Transition |
C>T |
All |
1941156 |
5.04 % |
| Transversion |
A>C |
All |
435074 |
1.13 % |
| Transversion |
C>A |
All |
1410244 |
3.66 % |
| Transversion |
T>G |
All |
556956 |
1.45 % |
| Transversion |
G>T |
All |
1293932 |
3.36 % |
| Transversion |
A>T |
All |
832738 |
2.16 % |
| Transversion |
T>A |
All |
987977 |
2.56 % |
| Transversion |
C>G |
All |
535110 |
1.39 % |
| Transversion |
G>C |
All |
512826 |
1.33 % |
| |
|
|
|
|
| Transition |
A>G |
Passed |
1096984 |
20.26 % |
| Transition |
G>A |
Passed |
637906 |
11.78 % |
| Transition |
T>C |
Passed |
1874636 |
34.61 % |
| Transition |
C>T |
Passed |
518642 |
9.58 % |
| Transversion |
A>C |
Passed |
146645 |
2.71 % |
| Transversion |
C>A |
Passed |
196864 |
3.63 % |
| Transversion |
T>G |
Passed |
168839 |
3.12 % |
| Transversion |
G>T |
Passed |
165129 |
3.05 % |
| Transversion |
A>T |
Passed |
132050 |
2.44 % |
| Transversion |
T>A |
Passed |
169145 |
3.12 % |
| Transversion |
C>G |
Passed |
155531 |
2.87 % |
| Transversion |
G>C |
Passed |
153458 |
2.83 % |
| |
|
|
|
|
| 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 |
4.87 |
31962364 |
6564857 |
| Passed |
3.21 |
4128168 |
1287661 |
| dbSNPAll |
0 |
0 |
0 |
| dbSNPPassed |
0 |
0 |
0 |