/EXTERNAL Roadmap/variants/K006535_K006536_2_lane_gembs
BACK
SAMPLE K006535_K006536_2_lane_gembs
Variant counts
| Type |
Total |
Pass |
% |
| SNPs |
1161305115 |
892896322 |
76.89 % |
| Multiallelic |
0 |
0 |
0.00 % |
VCF Filtering Stats
| Type |
#Sites |
% |
#Non-Variant Sites |
% |
#Variant Sites |
% |
| All |
1161305115 |
100% |
1142659124 |
98.39 % |
18645991 |
1.61 % |
| |
|
|
|
|
|
|
| Passed |
895676071 |
77.13 % |
890795315 |
77.96 % |
4880756 |
0.54 % |
| Filtered |
265629044 |
22.87 % |
251863809 |
22.04 % |
13765235 |
1.54 % |
| |
|
|
|
|
|
|
| q20 |
190593652 |
71.75 % |
187141048 |
74.30 % |
3452604 |
25.08 % |
| qd2 |
18924502 |
7.12 % |
18635978 |
7.40 % |
288524 |
2.10 % |
| mq40 |
18641488 |
7.02 % |
18178464 |
7.22 % |
463024 |
3.36 % |
| q20,qd2 |
17704755 |
6.67 % |
8969073 |
3.56 % |
8735682 |
63.46 % |
| q20,mq40 |
15902456 |
5.99 % |
15631005 |
6.21 % |
271451 |
1.97 % |
| q20,qd2,mq40 |
3501293 |
1.32 % |
2987840 |
1.19 % |
513453 |
3.73 % |
| qd2,mq40 |
349619 |
0.13 % |
320401 |
0.13 % |
29218 |
0.21 % |
| q20,qd2,fs60 |
2943 |
0.00 % |
0 |
0.00 % |
2943 |
0.02 % |
| qd2,fs60 |
2824 |
0.00 % |
0 |
0.00 % |
2824 |
0.02 % |
| fs60 |
2334 |
0.00 % |
0 |
0.00 % |
2334 |
0.02 % |
| qd2,fs60,mq40 |
1963 |
0.00 % |
0 |
0.00 % |
1963 |
0.01 % |
| fs60,mq40 |
725 |
0.00 % |
0 |
0.00 % |
725 |
0.01 % |
| q20,qd2,fs60,mq40 |
481 |
0.00 % |
0 |
0.00 % |
481 |
0.00 % |
| q20,fs60 |
7 |
0.00 % |
0 |
0.00 % |
7 |
0.00 % |
| q20,fs60,mq40 |
2 |
0.00 % |
0 |
0.00 % |
2 |
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 |
5389920 |
22.31 % |
| Transition |
G>A |
All |
4575383 |
18.94 % |
| Transition |
T>C |
All |
6305207 |
26.10 % |
| Transition |
C>T |
All |
4212897 |
17.44 % |
| Transversion |
A>C |
All |
339997 |
1.41 % |
| Transversion |
C>A |
All |
598454 |
2.48 % |
| Transversion |
T>G |
All |
369534 |
1.53 % |
| Transversion |
G>T |
All |
590265 |
2.44 % |
| Transversion |
A>T |
All |
627319 |
2.60 % |
| Transversion |
T>A |
All |
613811 |
2.54 % |
| Transversion |
C>G |
All |
273583 |
1.13 % |
| Transversion |
G>C |
All |
258932 |
1.07 % |
| |
|
|
|
|
| Transition |
A>G |
Passed |
578692 |
19.00 % |
| Transition |
G>A |
Passed |
482205 |
15.83 % |
| Transition |
T>C |
Passed |
613983 |
20.16 % |
| Transition |
C>T |
Passed |
480982 |
15.79 % |
| Transversion |
A>C |
Passed |
117431 |
3.85 % |
| Transversion |
C>A |
Passed |
111045 |
3.65 % |
| Transversion |
T>G |
Passed |
117669 |
3.86 % |
| Transversion |
G>T |
Passed |
111452 |
3.66 % |
| Transversion |
A>T |
Passed |
89160 |
2.93 % |
| Transversion |
T>A |
Passed |
88838 |
2.92 % |
| Transversion |
C>G |
Passed |
126998 |
4.17 % |
| Transversion |
G>C |
Passed |
127766 |
4.19 % |
| |
|
|
|
|
| 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 |
5.58 |
20483407 |
3671895 |
| Passed |
2.42 |
2155862 |
890359 |
| dbSNPAll |
0 |
0 |
0 |
| dbSNPPassed |
0 |
0 |
0 |