/EXTERNAL ENCODE/variants/K005733_K005726_2_lane_gembs
BACK
SAMPLE K005733_K005726_2_lane_gembs
Variant counts
| Type |
Total |
Pass |
% |
| SNPs |
1155890734 |
1071061320 |
92.66 % |
| Multiallelic |
0 |
0 |
0.00 % |
VCF Filtering Stats
| Type |
#Sites |
% |
#Non-Variant Sites |
% |
#Variant Sites |
% |
| All |
1155890734 |
100% |
1145893513 |
99.14 % |
9997221 |
0.86 % |
| |
|
|
|
|
|
|
| Passed |
1071494142 |
92.70 % |
1068848803 |
93.28 % |
2645339 |
0.25 % |
| Filtered |
84396592 |
7.30 % |
77044710 |
6.72 % |
7351882 |
0.69 % |
| |
|
|
|
|
|
|
| q20 |
45643869 |
54.08 % |
44831727 |
58.19 % |
812142 |
11.05 % |
| q20,mq40 |
13859683 |
16.42 % |
13547653 |
17.58 % |
312030 |
4.24 % |
| q20,qd2 |
9664624 |
11.45 % |
4556949 |
5.91 % |
5107675 |
69.47 % |
| qd2 |
6672888 |
7.91 % |
6246161 |
8.11 % |
426727 |
5.80 % |
| mq40 |
4850060 |
5.75 % |
4552181 |
5.91 % |
297879 |
4.05 % |
| q20,qd2,mq40 |
3613294 |
4.28 % |
3235782 |
4.20 % |
377512 |
5.13 % |
| qd2,mq40 |
89749 |
0.11 % |
74257 |
0.10 % |
15492 |
0.21 % |
| qd2,fs60,mq40 |
1020 |
0.00 % |
0 |
0.00 % |
1020 |
0.01 % |
| fs60,mq40 |
420 |
0.00 % |
0 |
0.00 % |
420 |
0.01 % |
| fs60 |
415 |
0.00 % |
0 |
0.00 % |
415 |
0.01 % |
| qd2,fs60 |
380 |
0.00 % |
0 |
0.00 % |
380 |
0.01 % |
| q20,qd2,fs60,mq40 |
108 |
0.00 % |
0 |
0.00 % |
108 |
0.00 % |
| q20,qd2,fs60 |
76 |
0.00 % |
0 |
0.00 % |
76 |
0.00 % |
| q20,fs60,mq40 |
6 |
0.00 % |
0 |
0.00 % |
6 |
0.00 % |
| q20,fs60 |
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 |
3541872 |
29.44 % |
| Transition |
G>A |
All |
939837 |
7.81 % |
| Transition |
T>C |
All |
3385379 |
28.14 % |
| Transition |
C>T |
All |
959838 |
7.98 % |
| Transversion |
A>C |
All |
302190 |
2.51 % |
| Transversion |
C>A |
All |
498737 |
4.15 % |
| Transversion |
T>G |
All |
305760 |
2.54 % |
| Transversion |
G>T |
All |
499610 |
4.15 % |
| Transversion |
A>T |
All |
554208 |
4.61 % |
| Transversion |
T>A |
All |
549891 |
4.57 % |
| Transversion |
C>G |
All |
250202 |
2.08 % |
| Transversion |
G>C |
All |
244462 |
2.03 % |
| |
|
|
|
|
| Transition |
A>G |
Passed |
686833 |
18.93 % |
| Transition |
G>A |
Passed |
544071 |
15.00 % |
| Transition |
T>C |
Passed |
677802 |
18.69 % |
| Transition |
C>T |
Passed |
545974 |
15.05 % |
| Transversion |
A>C |
Passed |
148360 |
4.09 % |
| Transversion |
C>A |
Passed |
155316 |
4.28 % |
| Transversion |
T>G |
Passed |
149462 |
4.12 % |
| Transversion |
G>T |
Passed |
155436 |
4.29 % |
| Transversion |
A>T |
Passed |
136339 |
3.76 % |
| Transversion |
T>A |
Passed |
137321 |
3.79 % |
| Transversion |
C>G |
Passed |
145175 |
4.00 % |
| Transversion |
G>C |
Passed |
145304 |
4.01 % |
| |
|
|
|
|
| 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 |
2.75 |
8826926 |
3205060 |
| Passed |
2.09 |
2454680 |
1172713 |
| dbSNPAll |
0 |
0 |
0 |
| dbSNPPassed |
0 |
0 |
0 |