/EXTERNAL ENCODE/variants/K005735_K005710_2_lane_gembs
BACK
SAMPLE K005735_K005710_2_lane_gembs
Variant counts
| Type |
Total |
Pass |
% |
| SNPs |
1164000973 |
1098053342 |
94.33 % |
| Multiallelic |
0 |
0 |
0.00 % |
VCF Filtering Stats
| Type |
#Sites |
% |
#Non-Variant Sites |
% |
#Variant Sites |
% |
| All |
1164000973 |
100% |
1155078352 |
99.23 % |
8922621 |
0.77 % |
| |
|
|
|
|
|
|
| Passed |
1098585849 |
94.38 % |
1095063816 |
94.80 % |
3522033 |
0.32 % |
| Filtered |
65415124 |
5.62 % |
60014536 |
5.20 % |
5400588 |
0.49 % |
| |
|
|
|
|
|
|
| q20 |
37970834 |
58.05 % |
37573898 |
62.61 % |
396936 |
7.35 % |
| q20,mq40 |
10463608 |
16.00 % |
10270810 |
17.11 % |
192798 |
3.57 % |
| mq40 |
5590814 |
8.55 % |
5201282 |
8.67 % |
389532 |
7.21 % |
| q20,qd2 |
5544293 |
8.48 % |
1863056 |
3.10 % |
3681237 |
68.16 % |
| qd2 |
2902966 |
4.44 % |
2485594 |
4.14 % |
417372 |
7.73 % |
| q20,qd2,mq40 |
2797463 |
4.28 % |
2505351 |
4.17 % |
292112 |
5.41 % |
| qd2,mq40 |
140426 |
0.21 % |
114545 |
0.19 % |
25881 |
0.48 % |
| qd2,fs60,mq40 |
1750 |
0.00 % |
0 |
0.00 % |
1750 |
0.03 % |
| fs60 |
1049 |
0.00 % |
0 |
0.00 % |
1049 |
0.02 % |
| qd2,fs60 |
934 |
0.00 % |
0 |
0.00 % |
934 |
0.02 % |
| fs60,mq40 |
545 |
0.00 % |
0 |
0.00 % |
545 |
0.01 % |
| q20,qd2,fs60 |
278 |
0.00 % |
0 |
0.00 % |
278 |
0.01 % |
| q20,qd2,fs60,mq40 |
149 |
0.00 % |
0 |
0.00 % |
149 |
0.00 % |
| q20,fs60 |
12 |
0.00 % |
0 |
0.00 % |
12 |
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 |
3096376 |
28.02 % |
| Transition |
G>A |
All |
1019195 |
9.22 % |
| Transition |
T>C |
All |
2958342 |
26.77 % |
| Transition |
C>T |
All |
1037830 |
9.39 % |
| Transversion |
A>C |
All |
314215 |
2.84 % |
| Transversion |
C>A |
All |
444341 |
4.02 % |
| Transversion |
T>G |
All |
327635 |
2.96 % |
| Transversion |
G>T |
All |
438955 |
3.97 % |
| Transversion |
A>T |
All |
395234 |
3.58 % |
| Transversion |
T>A |
All |
405758 |
3.67 % |
| Transversion |
C>G |
All |
310798 |
2.81 % |
| Transversion |
G>C |
All |
303830 |
2.75 % |
| |
|
|
|
|
| Transition |
A>G |
Passed |
804842 |
17.53 % |
| Transition |
G>A |
Passed |
715347 |
15.58 % |
| Transition |
T>C |
Passed |
814169 |
17.73 % |
| Transition |
C>T |
Passed |
718271 |
15.64 % |
| Transversion |
A>C |
Passed |
193904 |
4.22 % |
| Transversion |
C>A |
Passed |
209060 |
4.55 % |
| Transversion |
T>G |
Passed |
194961 |
4.25 % |
| Transversion |
G>T |
Passed |
199482 |
4.34 % |
| Transversion |
A>T |
Passed |
178080 |
3.88 % |
| Transversion |
T>A |
Passed |
181409 |
3.95 % |
| Transversion |
C>G |
Passed |
191710 |
4.17 % |
| Transversion |
G>C |
Passed |
191261 |
4.16 % |
| |
|
|
|
|
| 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 |
2.76 |
8111743 |
2940766 |
| Passed |
1.98 |
3052629 |
1539867 |
| dbSNPAll |
0 |
0 |
0 |
| dbSNPPassed |
0 |
0 |
0 |