/EXTERNAL Roadmap/variants/K006534_1_lane_gembs
BACK
SAMPLE K006534_1_lane_gembs
Variant counts
| Type |
Total |
Pass |
% |
| SNPs |
1156674583 |
1069259730 |
92.44 % |
| Multiallelic |
0 |
0 |
0.00 % |
VCF Filtering Stats
| Type |
#Sites |
% |
#Non-Variant Sites |
% |
#Variant Sites |
% |
| All |
1156674583 |
100% |
1148966730 |
99.33 % |
7707853 |
0.67 % |
| |
|
|
|
|
|
|
| Passed |
1069473177 |
92.46 % |
1066433915 |
92.82 % |
3039262 |
0.28 % |
| Filtered |
87201406 |
7.54 % |
82532815 |
7.18 % |
4668591 |
0.44 % |
| |
|
|
|
|
|
|
| mq40 |
44796430 |
51.37 % |
44214390 |
53.57 % |
582040 |
12.47 % |
| q20,mq40 |
17850387 |
20.47 % |
17611235 |
21.34 % |
239152 |
5.12 % |
| q20 |
16903470 |
19.38 % |
16582985 |
20.09 % |
320485 |
6.86 % |
| q20,qd2 |
3229561 |
3.70 % |
769377 |
0.93 % |
2460184 |
52.70 % |
| q20,qd2,mq40 |
2435675 |
2.79 % |
1817044 |
2.20 % |
618631 |
13.25 % |
| qd2 |
1593416 |
1.83 % |
1281334 |
1.55 % |
312082 |
6.68 % |
| qd2,mq40 |
322876 |
0.37 % |
256450 |
0.31 % |
66426 |
1.42 % |
| fs60 |
33719 |
0.04 % |
0 |
0.00 % |
33719 |
0.72 % |
| q20,qd2,fs60 |
13611 |
0.02 % |
0 |
0.00 % |
13611 |
0.29 % |
| fs60,mq40 |
12651 |
0.01 % |
0 |
0.00 % |
12651 |
0.27 % |
| q20,fs60 |
4662 |
0.01 % |
0 |
0.00 % |
4662 |
0.10 % |
| qd2,fs60 |
3341 |
0.00 % |
0 |
0.00 % |
3341 |
0.07 % |
| qd2,fs60,mq40 |
771 |
0.00 % |
0 |
0.00 % |
771 |
0.02 % |
| q20,qd2,fs60,mq40 |
729 |
0.00 % |
0 |
0.00 % |
729 |
0.02 % |
| q20,fs60,mq40 |
107 |
0.00 % |
0 |
0.00 % |
107 |
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 |
2510398 |
27.16 % |
| Transition |
G>A |
All |
946958 |
10.24 % |
| Transition |
T>C |
All |
2515283 |
27.21 % |
| Transition |
C>T |
All |
953175 |
10.31 % |
| Transversion |
A>C |
All |
251548 |
2.72 % |
| Transversion |
C>A |
All |
353759 |
3.83 % |
| Transversion |
T>G |
All |
256417 |
2.77 % |
| Transversion |
G>T |
All |
358372 |
3.88 % |
| Transversion |
A>T |
All |
330971 |
3.58 % |
| Transversion |
T>A |
All |
320751 |
3.47 % |
| Transversion |
C>G |
All |
222283 |
2.40 % |
| Transversion |
G>C |
All |
223667 |
2.42 % |
| |
|
|
|
|
| Transition |
A>G |
Passed |
760936 |
18.78 % |
| Transition |
G>A |
Passed |
621749 |
15.35 % |
| Transition |
T>C |
Passed |
782417 |
19.31 % |
| Transition |
C>T |
Passed |
629826 |
15.55 % |
| Transversion |
A>C |
Passed |
169002 |
4.17 % |
| Transversion |
C>A |
Passed |
156367 |
3.86 % |
| Transversion |
T>G |
Passed |
169634 |
4.19 % |
| Transversion |
G>T |
Passed |
157446 |
3.89 % |
| Transversion |
A>T |
Passed |
142551 |
3.52 % |
| Transversion |
T>A |
Passed |
141592 |
3.50 % |
| Transversion |
C>G |
Passed |
159197 |
3.93 % |
| Transversion |
G>C |
Passed |
160428 |
3.96 % |
| |
|
|
|
|
| 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 |
2.99 |
6925814 |
2317768 |
| Passed |
2.22 |
2794928 |
1256217 |
| dbSNPAll |
0 |
0 |
0 |
| dbSNPPassed |
0 |
0 |
0 |