/EXTERNAL DEEP/variants/K009028_K009029_K009030_3_lane_gembs
BACK
SAMPLE K009028_K009029_K009030_3_lane_gembs
Variant counts
| Type |
Total |
Pass |
% |
| SNPs |
1170862247 |
704188250 |
60.14 % |
| Multiallelic |
0 |
0 |
0.00 % |
VCF Filtering Stats
| Type |
#Sites |
% |
#Non-Variant Sites |
% |
#Variant Sites |
% |
| All |
1170862247 |
100% |
1139971553 |
97.36 % |
30890694 |
2.64 % |
| |
|
|
|
|
|
|
| Passed |
709440930 |
60.59 % |
700501330 |
61.45 % |
8939600 |
1.26 % |
| Filtered |
461421317 |
39.41 % |
439470223 |
38.55 % |
21951094 |
3.09 % |
| |
|
|
|
|
|
|
| q20 |
419058897 |
90.82 % |
412081593 |
93.77 % |
6977304 |
31.79 % |
| q20,qd2 |
24999961 |
5.42 % |
10836075 |
2.47 % |
14163886 |
64.52 % |
| q20,mq40 |
9017389 |
1.95 % |
8854448 |
2.01 % |
162941 |
0.74 % |
| qd2 |
4310710 |
0.93 % |
3989885 |
0.91 % |
320825 |
1.46 % |
| q20,qd2,mq40 |
3057216 |
0.66 % |
2925936 |
0.67 % |
131280 |
0.60 % |
| mq40 |
939231 |
0.20 % |
752913 |
0.17 % |
186318 |
0.85 % |
| qd2,mq40 |
35431 |
0.01 % |
29373 |
0.01 % |
6058 |
0.03 % |
| qd2,fs60,mq40 |
832 |
0.00 % |
0 |
0.00 % |
832 |
0.00 % |
| qd2,fs60 |
559 |
0.00 % |
0 |
0.00 % |
559 |
0.00 % |
| fs60 |
331 |
0.00 % |
0 |
0.00 % |
331 |
0.00 % |
| q20,qd2,fs60 |
308 |
0.00 % |
0 |
0.00 % |
308 |
0.00 % |
| fs60,mq40 |
258 |
0.00 % |
0 |
0.00 % |
258 |
0.00 % |
| q20,qd2,fs60,mq40 |
192 |
0.00 % |
0 |
0.00 % |
192 |
0.00 % |
| q20,fs60 |
1 |
0.00 % |
0 |
0.00 % |
1 |
0.00 % |
| q20,fs60,mq40 |
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 |
10658801 |
32.42 % |
| Transition |
G>A |
All |
2302006 |
7.00 % |
| Transition |
T>C |
All |
12034994 |
36.60 % |
| Transition |
C>T |
All |
1832270 |
5.57 % |
| Transversion |
A>C |
All |
499665 |
1.52 % |
| Transversion |
C>A |
All |
1230054 |
3.74 % |
| Transversion |
T>G |
All |
570381 |
1.73 % |
| Transversion |
G>T |
All |
1153718 |
3.51 % |
| Transversion |
A>T |
All |
779752 |
2.37 % |
| Transversion |
T>A |
All |
845432 |
2.57 % |
| Transversion |
C>G |
All |
500745 |
1.52 % |
| Transversion |
G>C |
All |
472433 |
1.44 % |
| |
|
|
|
|
| Transition |
A>G |
Passed |
903470 |
20.16 % |
| Transition |
G>A |
Passed |
541965 |
12.10 % |
| Transition |
T>C |
Passed |
1378909 |
30.78 % |
| Transition |
C>T |
Passed |
484890 |
10.82 % |
| Transversion |
A>C |
Passed |
142328 |
3.18 % |
| Transversion |
C>A |
Passed |
174246 |
3.89 % |
| Transversion |
T>G |
Passed |
158228 |
3.53 % |
| Transversion |
G>T |
Passed |
155749 |
3.48 % |
| Transversion |
A>T |
Passed |
120910 |
2.70 % |
| Transversion |
T>A |
Passed |
137862 |
3.08 % |
| Transversion |
C>G |
Passed |
142764 |
3.19 % |
| Transversion |
G>C |
Passed |
139204 |
3.11 % |
| |
|
|
|
|
| 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 |
4.43 |
26828071 |
6052180 |
| Passed |
2.83 |
3309234 |
1171291 |
| dbSNPAll |
0 |
0 |
0 |
| dbSNPPassed |
0 |
0 |
0 |