/EXTERNAL EpiHK/variants/K006632_1_lane_gembs
BACK
SAMPLE K006632_1_lane_gembs
Variant counts
| Type |
Total |
Pass |
% |
| SNPs |
1067702378 |
430324104 |
40.30 % |
| Multiallelic |
0 |
0 |
0.00 % |
VCF Filtering Stats
| Type |
#Sites |
% |
#Non-Variant Sites |
% |
#Variant Sites |
% |
| All |
1067702378 |
100% |
1045110490 |
97.88 % |
22591888 |
2.12 % |
| |
|
|
|
|
|
|
| Passed |
435236906 |
40.76 % |
429099473 |
41.06 % |
6137433 |
1.41 % |
| Filtered |
632465472 |
59.24 % |
616011017 |
58.94 % |
16454455 |
3.78 % |
| |
|
|
|
|
|
|
| q20 |
528758909 |
83.60 % |
524364422 |
85.12 % |
4394487 |
26.71 % |
| q20,qd2 |
71721647 |
11.34 % |
60195914 |
9.77 % |
11525733 |
70.05 % |
| qd2 |
17732101 |
2.80 % |
17547945 |
2.85 % |
184156 |
1.12 % |
| q20,mq40 |
9186584 |
1.45 % |
9106030 |
1.48 % |
80554 |
0.49 % |
| q20,qd2,mq40 |
2964968 |
0.47 % |
2859813 |
0.46 % |
105155 |
0.64 % |
| mq40 |
2001322 |
0.32 % |
1870494 |
0.30 % |
130828 |
0.80 % |
| qd2,mq40 |
77796 |
0.01 % |
66399 |
0.01 % |
11397 |
0.07 % |
| qd2,fs60 |
10467 |
0.00 % |
0 |
0.00 % |
10467 |
0.06 % |
| q20,qd2,fs60 |
6648 |
0.00 % |
0 |
0.00 % |
6648 |
0.04 % |
| fs60 |
2453 |
0.00 % |
0 |
0.00 % |
2453 |
0.01 % |
| qd2,fs60,mq40 |
1658 |
0.00 % |
0 |
0.00 % |
1658 |
0.01 % |
| q20,qd2,fs60,mq40 |
532 |
0.00 % |
0 |
0.00 % |
532 |
0.00 % |
| fs60,mq40 |
385 |
0.00 % |
0 |
0.00 % |
385 |
0.00 % |
| q20,fs60 |
2 |
0.00 % |
0 |
0.00 % |
2 |
0.00 % |
| q20,fs60,mq40 |
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 |
7906616 |
22.85 % |
| Transition |
G>A |
All |
8812696 |
25.47 % |
| Transition |
T>C |
All |
4902804 |
14.17 % |
| Transition |
C>T |
All |
8873299 |
25.64 % |
| Transversion |
A>C |
All |
356872 |
1.03 % |
| Transversion |
C>A |
All |
692351 |
2.00 % |
| Transversion |
T>G |
All |
644839 |
1.86 % |
| Transversion |
G>T |
All |
568962 |
1.64 % |
| Transversion |
A>T |
All |
451870 |
1.31 % |
| Transversion |
T>A |
All |
668826 |
1.93 % |
| Transversion |
C>G |
All |
430262 |
1.24 % |
| Transversion |
G>C |
All |
297155 |
0.86 % |
| |
|
|
|
|
| Transition |
A>G |
Passed |
377798 |
22.76 % |
| Transition |
G>A |
Passed |
249975 |
15.06 % |
| Transition |
T>C |
Passed |
364942 |
21.98 % |
| Transition |
C>T |
Passed |
251673 |
15.16 % |
| Transversion |
A>C |
Passed |
53926 |
3.25 % |
| Transversion |
C>A |
Passed |
49938 |
3.01 % |
| Transversion |
T>G |
Passed |
56304 |
3.39 % |
| Transversion |
G>T |
Passed |
49929 |
3.01 % |
| Transversion |
A>T |
Passed |
30853 |
1.86 % |
| Transversion |
T>A |
Passed |
30283 |
1.82 % |
| Transversion |
C>G |
Passed |
72755 |
4.38 % |
| Transversion |
G>C |
Passed |
71648 |
4.32 % |
| |
|
|
|
|
| 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 |
7.42 |
30495415 |
4111137 |
| Passed |
2.99 |
1244388 |
415636 |
| dbSNPAll |
0 |
0 |
0 |
| dbSNPPassed |
0 |
0 |
0 |