/EXTERNAL ENCODE/variants/K005738_K005721_2_lane_gembs
BACK
SAMPLE K005738_K005721_2_lane_gembs
Variant counts
| Type |
Total |
Pass |
% |
| SNPs |
1170490658 |
1111924572 |
95.00 % |
| Multiallelic |
0 |
0 |
0.00 % |
VCF Filtering Stats
| Type |
#Sites |
% |
#Non-Variant Sites |
% |
#Variant Sites |
% |
| All |
1170490658 |
100% |
1162549707 |
99.32 % |
7940951 |
0.68 % |
| |
|
|
|
|
|
|
| Passed |
1112418746 |
95.04 % |
1109028309 |
95.40 % |
3390437 |
0.30 % |
| Filtered |
58071912 |
4.96 % |
53521398 |
4.60 % |
4550514 |
0.41 % |
| |
|
|
|
|
|
|
| q20 |
33952357 |
58.47 % |
33585240 |
62.75 % |
367117 |
8.07 % |
| q20,mq40 |
9187615 |
15.82 % |
9037387 |
16.89 % |
150228 |
3.30 % |
| mq40 |
5377418 |
9.26 % |
5013949 |
9.37 % |
363469 |
7.99 % |
| q20,qd2 |
4425831 |
7.62 % |
1404579 |
2.62 % |
3021252 |
66.39 % |
| qd2 |
2532634 |
4.36 % |
2161224 |
4.04 % |
371410 |
8.16 % |
| q20,qd2,mq40 |
2440193 |
4.20 % |
2197047 |
4.10 % |
243146 |
5.34 % |
| qd2,mq40 |
148382 |
0.26 % |
121972 |
0.23 % |
26410 |
0.58 % |
| qd2,fs60,mq40 |
2114 |
0.00 % |
0 |
0.00 % |
2114 |
0.05 % |
| fs60 |
2000 |
0.00 % |
0 |
0.00 % |
2000 |
0.04 % |
| qd2,fs60 |
1995 |
0.00 % |
0 |
0.00 % |
1995 |
0.04 % |
| fs60,mq40 |
662 |
0.00 % |
0 |
0.00 % |
662 |
0.01 % |
| q20,qd2,fs60 |
506 |
0.00 % |
0 |
0.00 % |
506 |
0.01 % |
| q20,qd2,fs60,mq40 |
180 |
0.00 % |
0 |
0.00 % |
180 |
0.00 % |
| q20,fs60 |
13 |
0.00 % |
0 |
0.00 % |
13 |
0.00 % |
| q20,fs60,mq40 |
12 |
0.00 % |
0 |
0.00 % |
12 |
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 |
2722866 |
27.97 % |
| Transition |
G>A |
All |
936986 |
9.62 % |
| Transition |
T>C |
All |
2586690 |
26.57 % |
| Transition |
C>T |
All |
955466 |
9.81 % |
| Transversion |
A>C |
All |
266984 |
2.74 % |
| Transversion |
C>A |
All |
374137 |
3.84 % |
| Transversion |
T>G |
All |
280548 |
2.88 % |
| Transversion |
G>T |
All |
374493 |
3.85 % |
| Transversion |
A>T |
All |
343787 |
3.53 % |
| Transversion |
T>A |
All |
350729 |
3.60 % |
| Transversion |
C>G |
All |
275018 |
2.82 % |
| Transversion |
G>C |
All |
267541 |
2.75 % |
| |
|
|
|
|
| Transition |
A>G |
Passed |
755315 |
17.81 % |
| Transition |
G>A |
Passed |
667930 |
15.75 % |
| Transition |
T>C |
Passed |
748858 |
17.66 % |
| Transition |
C>T |
Passed |
669274 |
15.78 % |
| Transversion |
A>C |
Passed |
176646 |
4.17 % |
| Transversion |
C>A |
Passed |
183736 |
4.33 % |
| Transversion |
T>G |
Passed |
178358 |
4.21 % |
| Transversion |
G>T |
Passed |
178151 |
4.20 % |
| Transversion |
A>T |
Passed |
163867 |
3.86 % |
| Transversion |
T>A |
Passed |
165681 |
3.91 % |
| Transversion |
C>G |
Passed |
176203 |
4.16 % |
| Transversion |
G>C |
Passed |
176087 |
4.15 % |
| |
|
|
|
|
| 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 |
2.84 |
7202008 |
2533237 |
| Passed |
2.03 |
2841377 |
1398729 |
| dbSNPAll |
0 |
0 |
0 |
| dbSNPPassed |
0 |
0 |
0 |