/EXTERNAL Roadmap/variants/K006479_K006480_2_lane_gembs
BACK
SAMPLE K006479_K006480_2_lane_gembs
Variant counts
| Type |
Total |
Pass |
% |
| SNPs |
1150460661 |
1068707977 |
92.89 % |
| Multiallelic |
0 |
0 |
0.00 % |
VCF Filtering Stats
| Type |
#Sites |
% |
#Non-Variant Sites |
% |
#Variant Sites |
% |
| All |
1150460661 |
100% |
1143723786 |
99.41 % |
6736875 |
0.59 % |
| |
|
|
|
|
|
|
| Passed |
1068866721 |
92.91 % |
1065980769 |
93.20 % |
2885952 |
0.27 % |
| Filtered |
81593940 |
7.09 % |
77743017 |
6.80 % |
3850923 |
0.36 % |
| |
|
|
|
|
|
|
| mq40 |
43020361 |
52.72 % |
42467422 |
54.63 % |
552939 |
14.36 % |
| q20,mq40 |
17992767 |
22.05 % |
17746695 |
22.83 % |
246072 |
6.39 % |
| q20 |
13704813 |
16.80 % |
13457397 |
17.31 % |
247416 |
6.42 % |
| q20,qd2 |
2531266 |
3.10 % |
687378 |
0.88 % |
1843888 |
47.88 % |
| q20,qd2,mq40 |
2465660 |
3.02 % |
1881181 |
2.42 % |
584479 |
15.18 % |
| qd2 |
1547731 |
1.90 % |
1295787 |
1.67 % |
251944 |
6.54 % |
| qd2,mq40 |
262701 |
0.32 % |
207157 |
0.27 % |
55544 |
1.44 % |
| q20,qd2,fs60 |
25692 |
0.03 % |
0 |
0.00 % |
25692 |
0.67 % |
| fs60 |
25246 |
0.03 % |
0 |
0.00 % |
25246 |
0.66 % |
| fs60,mq40 |
7534 |
0.01 % |
0 |
0.00 % |
7534 |
0.20 % |
| q20,fs60 |
6914 |
0.01 % |
0 |
0.00 % |
6914 |
0.18 % |
| qd2,fs60 |
1867 |
0.00 % |
0 |
0.00 % |
1867 |
0.05 % |
| q20,qd2,fs60,mq40 |
849 |
0.00 % |
0 |
0.00 % |
849 |
0.02 % |
| qd2,fs60,mq40 |
389 |
0.00 % |
0 |
0.00 % |
389 |
0.01 % |
| q20,fs60,mq40 |
150 |
0.00 % |
0 |
0.00 % |
150 |
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 |
2100046 |
25.34 % |
| Transition |
G>A |
All |
894588 |
10.79 % |
| Transition |
T>C |
All |
2111159 |
25.47 % |
| Transition |
C>T |
All |
911183 |
10.99 % |
| Transversion |
A>C |
All |
227816 |
2.75 % |
| Transversion |
C>A |
All |
345471 |
4.17 % |
| Transversion |
T>G |
All |
225747 |
2.72 % |
| Transversion |
G>T |
All |
343381 |
4.14 % |
| Transversion |
A>T |
All |
352804 |
4.26 % |
| Transversion |
T>A |
All |
342145 |
4.13 % |
| Transversion |
C>G |
All |
215277 |
2.60 % |
| Transversion |
G>C |
All |
219169 |
2.64 % |
| |
|
|
|
|
| Transition |
A>G |
Passed |
727408 |
18.44 % |
| Transition |
G>A |
Passed |
617811 |
15.66 % |
| Transition |
T>C |
Passed |
734313 |
18.61 % |
| Transition |
C>T |
Passed |
627824 |
15.91 % |
| Transversion |
A>C |
Passed |
160122 |
4.06 % |
| Transversion |
C>A |
Passed |
156779 |
3.97 % |
| Transversion |
T>G |
Passed |
160778 |
4.08 % |
| Transversion |
G>T |
Passed |
158178 |
4.01 % |
| Transversion |
A>T |
Passed |
143013 |
3.63 % |
| Transversion |
T>A |
Passed |
142124 |
3.60 % |
| Transversion |
C>G |
Passed |
157839 |
4.00 % |
| Transversion |
G>C |
Passed |
158904 |
4.03 % |
| |
|
|
|
|
| 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 |
2.65 |
6016976 |
2271810 |
| Passed |
2.19 |
2707356 |
1237737 |
| dbSNPAll |
0 |
0 |
0 |
| dbSNPPassed |
0 |
0 |
0 |