/EXTERNAL ENCODE/variants/K005732_K005718_2_lane_gembs
BACK
SAMPLE K005732_K005718_2_lane_gembs
Variant counts
| Type |
Total |
Pass |
% |
| SNPs |
1170753521 |
961114313 |
82.09 % |
| Multiallelic |
0 |
0 |
0.00 % |
VCF Filtering Stats
| Type |
#Sites |
% |
#Non-Variant Sites |
% |
#Variant Sites |
% |
| All |
1170753521 |
100% |
1157905917 |
98.90 % |
12847604 |
1.10 % |
| |
|
|
|
|
|
|
| Passed |
962795241 |
82.24 % |
958171015 |
82.75 % |
4624226 |
0.48 % |
| Filtered |
207958280 |
17.76 % |
199734902 |
17.25 % |
8223378 |
0.85 % |
| |
|
|
|
|
|
|
| q20 |
175511268 |
84.40 % |
174134386 |
87.18 % |
1376882 |
16.74 % |
| q20,qd2 |
10518148 |
5.06 % |
4912945 |
2.46 % |
5605203 |
68.16 % |
| q20,mq40 |
10462602 |
5.03 % |
10262483 |
5.14 % |
200119 |
2.43 % |
| mq40 |
4453024 |
2.14 % |
4130901 |
2.07 % |
322123 |
3.92 % |
| qd2 |
4025595 |
1.94 % |
3588317 |
1.80 % |
437278 |
5.32 % |
| q20,qd2,mq40 |
2867999 |
1.38 % |
2613960 |
1.31 % |
254039 |
3.09 % |
| qd2,mq40 |
112646 |
0.05 % |
91910 |
0.05 % |
20736 |
0.25 % |
| qd2,fs60 |
2058 |
0.00 % |
0 |
0.00 % |
2058 |
0.03 % |
| qd2,fs60,mq40 |
1820 |
0.00 % |
0 |
0.00 % |
1820 |
0.02 % |
| fs60 |
1764 |
0.00 % |
0 |
0.00 % |
1764 |
0.02 % |
| q20,qd2,fs60 |
731 |
0.00 % |
0 |
0.00 % |
731 |
0.01 % |
| fs60,mq40 |
418 |
0.00 % |
0 |
0.00 % |
418 |
0.01 % |
| q20,qd2,fs60,mq40 |
194 |
0.00 % |
0 |
0.00 % |
194 |
0.00 % |
| q20,fs60 |
10 |
0.00 % |
0 |
0.00 % |
10 |
0.00 % |
| q20,fs60,mq40 |
3 |
0.00 % |
0 |
0.00 % |
3 |
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 |
4616579 |
31.77 % |
| Transition |
G>A |
All |
1156932 |
7.96 % |
| Transition |
T>C |
All |
4093771 |
28.18 % |
| Transition |
C>T |
All |
1234964 |
8.50 % |
| Transversion |
A>C |
All |
413667 |
2.85 % |
| Transversion |
C>A |
All |
484887 |
3.34 % |
| Transversion |
T>G |
All |
429036 |
2.95 % |
| Transversion |
G>T |
All |
475660 |
3.27 % |
| Transversion |
A>T |
All |
385001 |
2.65 % |
| Transversion |
T>A |
All |
398226 |
2.74 % |
| Transversion |
C>G |
All |
428273 |
2.95 % |
| Transversion |
G>C |
All |
412020 |
2.84 % |
| |
|
|
|
|
| Transition |
A>G |
Passed |
706072 |
18.40 % |
| Transition |
G>A |
Passed |
584621 |
15.23 % |
| Transition |
T>C |
Passed |
681276 |
17.75 % |
| Transition |
C>T |
Passed |
588394 |
15.33 % |
| Transversion |
A>C |
Passed |
162229 |
4.23 % |
| Transversion |
C>A |
Passed |
170274 |
4.44 % |
| Transversion |
T>G |
Passed |
163012 |
4.25 % |
| Transversion |
G>T |
Passed |
165123 |
4.30 % |
| Transversion |
A>T |
Passed |
150642 |
3.92 % |
| Transversion |
T>A |
Passed |
152039 |
3.96 % |
| Transversion |
C>G |
Passed |
157392 |
4.10 % |
| Transversion |
G>C |
Passed |
157250 |
4.10 % |
| |
|
|
|
|
| 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 |
3.24 |
11102246 |
3426770 |
| Passed |
2.00 |
2560363 |
1277961 |
| dbSNPAll |
0 |
0 |
0 |
| dbSNPPassed |
0 |
0 |
0 |