/EXTERNAL KNIH/variants/K006241_1_lane_gembs
BACK
SAMPLE K006241_1_lane_gembs
Variant counts
| Type |
Total |
Pass |
% |
| SNPs |
1195643605 |
695448813 |
58.17 % |
| Multiallelic |
0 |
0 |
0.00 % |
VCF Filtering Stats
| Type |
#Sites |
% |
#Non-Variant Sites |
% |
#Variant Sites |
% |
| All |
1195643605 |
100% |
1134612334 |
94.90 % |
61031271 |
5.10 % |
| |
|
|
|
|
|
|
| Passed |
706915669 |
59.12 % |
686530472 |
60.51 % |
20385197 |
2.88 % |
| Filtered |
488727936 |
40.88 % |
448081862 |
39.49 % |
40646074 |
5.75 % |
| |
|
|
|
|
|
|
| q20 |
421744637 |
86.29 % |
407195359 |
90.88 % |
14549278 |
35.80 % |
| q20,qd2 |
49947244 |
10.22 % |
25627346 |
5.72 % |
24319898 |
59.83 % |
| qd2 |
9344781 |
1.91 % |
7947577 |
1.77 % |
1397204 |
3.44 % |
| q20,mq40 |
4942336 |
1.01 % |
4802710 |
1.07 % |
139626 |
0.34 % |
| q20,qd2,mq40 |
2166540 |
0.44 % |
2082595 |
0.46 % |
83945 |
0.21 % |
| mq40 |
558639 |
0.11 % |
410337 |
0.09 % |
148302 |
0.36 % |
| qd2,mq40 |
20672 |
0.00 % |
15938 |
0.00 % |
4734 |
0.01 % |
| fs60 |
1613 |
0.00 % |
0 |
0.00 % |
1613 |
0.00 % |
| q20,qd2,fs60 |
968 |
0.00 % |
0 |
0.00 % |
968 |
0.00 % |
| qd2,fs60 |
292 |
0.00 % |
0 |
0.00 % |
292 |
0.00 % |
| qd2,fs60,mq40 |
89 |
0.00 % |
0 |
0.00 % |
89 |
0.00 % |
| fs60,mq40 |
86 |
0.00 % |
0 |
0.00 % |
86 |
0.00 % |
| q20,fs60 |
21 |
0.00 % |
0 |
0.00 % |
21 |
0.00 % |
| q20,qd2,fs60,mq40 |
18 |
0.00 % |
0 |
0.00 % |
18 |
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 |
20815820 |
32.88 % |
| Transition |
G>A |
All |
4494934 |
7.10 % |
| Transition |
T>C |
All |
23223339 |
36.68 % |
| Transition |
C>T |
All |
3158072 |
4.99 % |
| Transversion |
A>C |
All |
1329087 |
2.10 % |
| Transversion |
C>A |
All |
1939196 |
3.06 % |
| Transversion |
T>G |
All |
1465881 |
2.32 % |
| Transversion |
G>T |
All |
1831374 |
2.89 % |
| Transversion |
A>T |
All |
1465422 |
2.31 % |
| Transversion |
T>A |
All |
1652458 |
2.61 % |
| Transversion |
C>G |
All |
967540 |
1.53 % |
| Transversion |
G>C |
All |
969846 |
1.53 % |
| |
|
|
|
|
| Transition |
A>G |
Passed |
2349008 |
24.46 % |
| Transition |
G>A |
Passed |
882252 |
9.19 % |
| Transition |
T>C |
Passed |
4065444 |
42.33 % |
| Transition |
C>T |
Passed |
651646 |
6.78 % |
| Transversion |
A>C |
Passed |
210914 |
2.20 % |
| Transversion |
C>A |
Passed |
241673 |
2.52 % |
| Transversion |
T>G |
Passed |
226139 |
2.35 % |
| Transversion |
G>T |
Passed |
195688 |
2.04 % |
| Transversion |
A>T |
Passed |
151115 |
1.57 % |
| Transversion |
T>A |
Passed |
199223 |
2.07 % |
| Transversion |
C>G |
Passed |
214391 |
2.23 % |
| Transversion |
G>C |
Passed |
217752 |
2.27 % |
| |
|
|
|
|
| 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 |
4.45 |
51692165 |
11620804 |
| Passed |
4.80 |
7948350 |
1656895 |
| dbSNPAll |
0 |
0 |
0 |
| dbSNPPassed |
0 |
0 |
0 |