/EXTERNAL Roadmap/variants/K006548_K006549_K006550_K006551_4_lane_gembs
BACK
SAMPLE K006548_K006549_K006550_K006551_4_lane_gembs
Variant counts
| Type |
Total |
Pass |
% |
| SNPs |
1167829405 |
860801782 |
73.71 % |
| Multiallelic |
0 |
0 |
0.00 % |
VCF Filtering Stats
| Type |
#Sites |
% |
#Non-Variant Sites |
% |
#Variant Sites |
% |
| All |
1167829405 |
100% |
1143478300 |
97.91 % |
24351105 |
2.09 % |
| |
|
|
|
|
|
|
| Passed |
864128909 |
73.99 % |
858139678 |
75.05 % |
5989231 |
0.69 % |
| Filtered |
303700496 |
26.01 % |
285338622 |
24.95 % |
18361874 |
2.12 % |
| |
|
|
|
|
|
|
| q20 |
219174212 |
72.17 % |
213658154 |
74.88 % |
5516058 |
30.04 % |
| q20,mq40 |
32578843 |
10.73 % |
32056327 |
11.23 % |
522516 |
2.85 % |
| mq40 |
27941136 |
9.20 % |
27241487 |
9.55 % |
699649 |
3.81 % |
| q20,qd2 |
15371473 |
5.06 % |
4777714 |
1.67 % |
10593759 |
57.69 % |
| qd2 |
4595039 |
1.51 % |
4365588 |
1.53 % |
229451 |
1.25 % |
| q20,qd2,mq40 |
3902021 |
1.28 % |
3132976 |
1.10 % |
769045 |
4.19 % |
| qd2,mq40 |
129354 |
0.04 % |
106376 |
0.04 % |
22978 |
0.13 % |
| fs60 |
4807 |
0.00 % |
0 |
0.00 % |
4807 |
0.03 % |
| fs60,mq40 |
1791 |
0.00 % |
0 |
0.00 % |
1791 |
0.01 % |
| q20,qd2,fs60 |
841 |
0.00 % |
0 |
0.00 % |
841 |
0.00 % |
| qd2,fs60 |
300 |
0.00 % |
0 |
0.00 % |
300 |
0.00 % |
| q20,fs60 |
277 |
0.00 % |
0 |
0.00 % |
277 |
0.00 % |
| q20,qd2,fs60,mq40 |
249 |
0.00 % |
0 |
0.00 % |
249 |
0.00 % |
| qd2,fs60,mq40 |
93 |
0.00 % |
0 |
0.00 % |
93 |
0.00 % |
| q20,fs60,mq40 |
60 |
0.00 % |
0 |
0.00 % |
60 |
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 |
8846597 |
33.77 % |
| Transition |
G>A |
All |
1680480 |
6.41 % |
| Transition |
T>C |
All |
10156630 |
38.77 % |
| Transition |
C>T |
All |
1511311 |
5.77 % |
| Transversion |
A>C |
All |
411675 |
1.57 % |
| Transversion |
C>A |
All |
597124 |
2.28 % |
| Transversion |
T>G |
All |
473192 |
1.81 % |
| Transversion |
G>T |
All |
601594 |
2.30 % |
| Transversion |
A>T |
All |
599820 |
2.29 % |
| Transversion |
T>A |
All |
587097 |
2.24 % |
| Transversion |
C>G |
All |
387361 |
1.48 % |
| Transversion |
G>C |
All |
344518 |
1.32 % |
| |
|
|
|
|
| Transition |
A>G |
Passed |
752648 |
21.02 % |
| Transition |
G>A |
Passed |
474265 |
13.24 % |
| Transition |
T>C |
Passed |
842916 |
23.54 % |
| Transition |
C>T |
Passed |
486601 |
13.59 % |
| Transversion |
A>C |
Passed |
139268 |
3.89 % |
| Transversion |
C>A |
Passed |
122800 |
3.43 % |
| Transversion |
T>G |
Passed |
141443 |
3.95 % |
| Transversion |
G>T |
Passed |
125201 |
3.50 % |
| Transversion |
A>T |
Passed |
108431 |
3.03 % |
| Transversion |
T>A |
Passed |
108017 |
3.02 % |
| Transversion |
C>G |
Passed |
140158 |
3.91 % |
| Transversion |
G>C |
Passed |
139190 |
3.89 % |
| |
|
|
|
|
| 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 |
5.55 |
22195018 |
4002381 |
| Passed |
2.50 |
2556430 |
1024508 |
| dbSNPAll |
0 |
0 |
0 |
| dbSNPPassed |
0 |
0 |
0 |