/EXTERNAL DEEP/variants/K008968_K008969_K008970_3_lane_gembs
BACK
SAMPLE K008968_K008969_K008970_3_lane_gembs
Variant counts
| Type |
Total |
Pass |
% |
| SNPs |
1175571222 |
793363432 |
67.49 % |
| Multiallelic |
0 |
0 |
0.00 % |
VCF Filtering Stats
| Type |
#Sites |
% |
#Non-Variant Sites |
% |
#Variant Sites |
% |
| All |
1175571222 |
100% |
1140608881 |
97.03 % |
34962341 |
2.97 % |
| |
|
|
|
|
|
|
| Passed |
798611214 |
67.93 % |
788883924 |
69.16 % |
9727290 |
1.22 % |
| Filtered |
376960008 |
32.07 % |
351724957 |
30.84 % |
25235051 |
3.16 % |
| |
|
|
|
|
|
|
| q20 |
332167888 |
88.12 % |
325498240 |
92.54 % |
6669648 |
26.43 % |
| q20,qd2 |
28141756 |
7.47 % |
10461973 |
2.97 % |
17679783 |
70.06 % |
| q20,mq40 |
8637834 |
2.29 % |
8503602 |
2.42 % |
134232 |
0.53 % |
| qd2 |
4262325 |
1.13 % |
3839157 |
1.09 % |
423168 |
1.68 % |
| q20,qd2,mq40 |
2763632 |
0.73 % |
2644240 |
0.75 % |
119392 |
0.47 % |
| mq40 |
956174 |
0.25 % |
754884 |
0.21 % |
201290 |
0.80 % |
| qd2,mq40 |
29029 |
0.01 % |
22861 |
0.01 % |
6168 |
0.02 % |
| qd2,fs60,mq40 |
501 |
0.00 % |
0 |
0.00 % |
501 |
0.00 % |
| qd2,fs60 |
266 |
0.00 % |
0 |
0.00 % |
266 |
0.00 % |
| fs60 |
237 |
0.00 % |
0 |
0.00 % |
237 |
0.00 % |
| fs60,mq40 |
198 |
0.00 % |
0 |
0.00 % |
198 |
0.00 % |
| q20,qd2,fs60,mq40 |
83 |
0.00 % |
0 |
0.00 % |
83 |
0.00 % |
| q20,qd2,fs60 |
82 |
0.00 % |
0 |
0.00 % |
82 |
0.00 % |
| q20,fs60 |
2 |
0.00 % |
0 |
0.00 % |
2 |
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 |
12067612 |
32.75 % |
| Transition |
G>A |
All |
2948442 |
8.00 % |
| Transition |
T>C |
All |
14219646 |
38.59 % |
| Transition |
C>T |
All |
1875679 |
5.09 % |
| Transversion |
A>C |
All |
392954 |
1.07 % |
| Transversion |
C>A |
All |
1194753 |
3.24 % |
| Transversion |
T>G |
All |
491057 |
1.33 % |
| Transversion |
G>T |
All |
1099965 |
2.99 % |
| Transversion |
A>T |
All |
750125 |
2.04 % |
| Transversion |
T>A |
All |
874968 |
2.37 % |
| Transversion |
C>G |
All |
468987 |
1.27 % |
| Transversion |
G>C |
All |
460289 |
1.25 % |
| |
|
|
|
|
| Transition |
A>G |
Passed |
1080271 |
20.13 % |
| Transition |
G>A |
Passed |
650741 |
12.13 % |
| Transition |
T>C |
Passed |
1833999 |
34.17 % |
| Transition |
C>T |
Passed |
528318 |
9.84 % |
| Transversion |
A>C |
Passed |
146478 |
2.73 % |
| Transversion |
C>A |
Passed |
193867 |
3.61 % |
| Transversion |
T>G |
Passed |
165381 |
3.08 % |
| Transversion |
G>T |
Passed |
160506 |
2.99 % |
| Transversion |
A>T |
Passed |
132095 |
2.46 % |
| Transversion |
T>A |
Passed |
167079 |
3.11 % |
| Transversion |
C>G |
Passed |
154735 |
2.88 % |
| Transversion |
G>C |
Passed |
153332 |
2.86 % |
| |
|
|
|
|
| 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 |
5.43 |
31111379 |
5733098 |
| Passed |
3.21 |
4093329 |
1273473 |
| dbSNPAll |
0 |
0 |
0 |
| dbSNPPassed |
0 |
0 |
0 |