/EXTERNAL DEEP/variants/K006055_K006056_K006123_K006124_K006125_5_lane_gembs
BACK
SAMPLE K006055_K006056_K006123_K006124_K006125_5_lane_gembs
Variant counts
| Type |
Total |
Pass |
% |
| SNPs |
1181357347 |
917914067 |
77.70 % |
| Multiallelic |
0 |
0 |
0.00 % |
VCF Filtering Stats
| Type |
#Sites |
% |
#Non-Variant Sites |
% |
#Variant Sites |
% |
| All |
1181357347 |
100% |
1136241638 |
96.18 % |
45115709 |
3.82 % |
| |
|
|
|
|
|
|
| Passed |
923895618 |
78.21 % |
912126986 |
80.28 % |
11768632 |
1.27 % |
| Filtered |
257461729 |
21.79 % |
224114652 |
19.72 % |
33347077 |
3.61 % |
| |
|
|
|
|
|
|
| q20 |
199132107 |
77.34 % |
192626394 |
85.95 % |
6505713 |
19.51 % |
| q20,qd2 |
35472517 |
13.78 % |
10309183 |
4.60 % |
25163334 |
75.46 % |
| q20,mq40 |
10497733 |
4.08 % |
10255025 |
4.58 % |
242708 |
0.73 % |
| qd2 |
7494393 |
2.91 % |
6602476 |
2.95 % |
891917 |
2.67 % |
| q20,qd2,mq40 |
3148728 |
1.22 % |
2931416 |
1.31 % |
217312 |
0.65 % |
| mq40 |
1676677 |
0.65 % |
1359515 |
0.61 % |
317162 |
0.95 % |
| qd2,mq40 |
38689 |
0.02 % |
30643 |
0.01 % |
8046 |
0.02 % |
| qd2,fs60,mq40 |
347 |
0.00 % |
0 |
0.00 % |
347 |
0.00 % |
| fs60,mq40 |
130 |
0.00 % |
0 |
0.00 % |
130 |
0.00 % |
| qd2,fs60 |
124 |
0.00 % |
0 |
0.00 % |
124 |
0.00 % |
| fs60 |
117 |
0.00 % |
0 |
0.00 % |
117 |
0.00 % |
| q20,qd2,fs60 |
114 |
0.00 % |
0 |
0.00 % |
114 |
0.00 % |
| q20,qd2,fs60,mq40 |
52 |
0.00 % |
0 |
0.00 % |
52 |
0.00 % |
| q20,fs60 |
1 |
0.00 % |
0 |
0.00 % |
1 |
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 |
17727872 |
37.71 % |
| Transition |
G>A |
All |
2678959 |
5.70 % |
| Transition |
T>C |
All |
19561572 |
41.61 % |
| Transition |
C>T |
All |
1973034 |
4.20 % |
| Transversion |
A>C |
All |
354460 |
0.75 % |
| Transversion |
C>A |
All |
1147030 |
2.44 % |
| Transversion |
T>G |
All |
418974 |
0.89 % |
| Transversion |
G>T |
All |
1064047 |
2.26 % |
| Transversion |
A>T |
All |
656474 |
1.40 % |
| Transversion |
T>A |
All |
737498 |
1.57 % |
| Transversion |
C>G |
All |
355671 |
0.76 % |
| Transversion |
G>C |
All |
337608 |
0.72 % |
| |
|
|
|
|
| Transition |
A>G |
Passed |
1572955 |
23.34 % |
| Transition |
G>A |
Passed |
672061 |
9.97 % |
| Transition |
T>C |
Passed |
2559533 |
37.98 % |
| Transition |
C>T |
Passed |
590306 |
8.76 % |
| Transversion |
A>C |
Passed |
151882 |
2.25 % |
| Transversion |
C>A |
Passed |
223717 |
3.32 % |
| Transversion |
T>G |
Passed |
164819 |
2.45 % |
| Transversion |
G>T |
Passed |
198044 |
2.94 % |
| Transversion |
A>T |
Passed |
135011 |
2.00 % |
| Transversion |
T>A |
Passed |
157991 |
2.34 % |
| Transversion |
C>G |
Passed |
158644 |
2.35 % |
| Transversion |
G>C |
Passed |
154242 |
2.29 % |
| |
|
|
|
|
| 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 |
8.27 |
41941437 |
5071762 |
| Passed |
4.01 |
5394855 |
1344350 |
| dbSNPAll |
0 |
0 |
0 |
| dbSNPPassed |
0 |
0 |
0 |