/EXTERNAL KNIH/variants/K006255_1_lane_gembs
BACK
SAMPLE K006255_1_lane_gembs
Variant counts
| Type |
Total |
Pass |
% |
| SNPs |
1107494875 |
403172983 |
36.40 % |
| Multiallelic |
0 |
0 |
0.00 % |
VCF Filtering Stats
| Type |
#Sites |
% |
#Non-Variant Sites |
% |
#Variant Sites |
% |
| All |
1107494875 |
100% |
1059403827 |
95.66 % |
48091048 |
4.34 % |
| |
|
|
|
|
|
|
| Passed |
413444240 |
37.33 % |
396967469 |
37.47 % |
16476771 |
3.99 % |
| Filtered |
694050635 |
62.67 % |
662436358 |
62.53 % |
31614277 |
7.65 % |
| |
|
|
|
|
|
|
| q20 |
605554147 |
87.25 % |
592145533 |
89.39 % |
13408614 |
42.41 % |
| q20,qd2 |
76572139 |
11.03 % |
59281962 |
8.95 % |
17290177 |
54.69 % |
| q20,mq40 |
4827718 |
0.70 % |
4726863 |
0.71 % |
100855 |
0.32 % |
| qd2 |
4078559 |
0.59 % |
3439219 |
0.52 % |
639340 |
2.02 % |
| q20,qd2,mq40 |
2595073 |
0.37 % |
2532689 |
0.38 % |
62384 |
0.20 % |
| mq40 |
402123 |
0.06 % |
294960 |
0.04 % |
107163 |
0.34 % |
| qd2,mq40 |
19668 |
0.00 % |
15132 |
0.00 % |
4536 |
0.01 % |
| q20,qd2,fs60 |
540 |
0.00 % |
0 |
0.00 % |
540 |
0.00 % |
| fs60 |
412 |
0.00 % |
0 |
0.00 % |
412 |
0.00 % |
| qd2,fs60 |
137 |
0.00 % |
0 |
0.00 % |
137 |
0.00 % |
| fs60,mq40 |
49 |
0.00 % |
0 |
0.00 % |
49 |
0.00 % |
| qd2,fs60,mq40 |
39 |
0.00 % |
0 |
0.00 % |
39 |
0.00 % |
| q20,qd2,fs60,mq40 |
22 |
0.00 % |
0 |
0.00 % |
22 |
0.00 % |
| q20,fs60 |
9 |
0.00 % |
0 |
0.00 % |
9 |
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 |
15423947 |
30.38 % |
| Transition |
G>A |
All |
3353243 |
6.60 % |
| Transition |
T>C |
All |
15371184 |
30.27 % |
| Transition |
C>T |
All |
2322271 |
4.57 % |
| Transversion |
A>C |
All |
1256988 |
2.48 % |
| Transversion |
C>A |
All |
2661506 |
5.24 % |
| Transversion |
T>G |
All |
1440490 |
2.84 % |
| Transversion |
G>T |
All |
2445752 |
4.82 % |
| Transversion |
A>T |
All |
2050158 |
4.04 % |
| Transversion |
T>A |
All |
2333889 |
4.60 % |
| Transversion |
C>G |
All |
1048526 |
2.06 % |
| Transversion |
G>C |
All |
1068712 |
2.10 % |
| |
|
|
|
|
| Transition |
A>G |
Passed |
1793933 |
27.35 % |
| Transition |
G>A |
Passed |
699679 |
10.67 % |
| Transition |
T>C |
Passed |
2372990 |
36.18 % |
| Transition |
C>T |
Passed |
443491 |
6.76 % |
| Transversion |
A>C |
Passed |
156920 |
2.39 % |
| Transversion |
C>A |
Passed |
181721 |
2.77 % |
| Transversion |
T>G |
Passed |
177592 |
2.71 % |
| Transversion |
G>T |
Passed |
125527 |
1.91 % |
| Transversion |
A>T |
Passed |
90919 |
1.39 % |
| Transversion |
T>A |
Passed |
143363 |
2.19 % |
| Transversion |
C>G |
Passed |
179250 |
2.73 % |
| Transversion |
G>C |
Passed |
194118 |
2.96 % |
| |
|
|
|
|
| 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 |
2.55 |
36470645 |
14306021 |
| Passed |
4.25 |
5310093 |
1249410 |
| dbSNPAll |
0 |
0 |
0 |
| dbSNPPassed |
0 |
0 |
0 |