/cemt/variants/K005742_0_lane_gembs
BACK
SAMPLE K005742_0_lane_gembs
Variant counts
| Type |
Total |
Pass |
% |
| SNPs |
1168231521 |
904526224 |
77.43 % |
| Multiallelic |
0 |
0 |
0.00 % |
VCF Filtering Stats
| Type |
#Sites |
% |
#Non-Variant Sites |
% |
#Variant Sites |
% |
| All |
1168231521 |
100% |
1152954811 |
98.69 % |
15276710 |
1.31 % |
| |
|
|
|
|
|
|
| Passed |
907467289 |
77.68 % |
901546133 |
78.19 % |
5921156 |
0.65 % |
| Filtered |
260764232 |
22.32 % |
251408678 |
21.81 % |
9355554 |
1.03 % |
| |
|
|
|
|
|
|
| q20 |
232408488 |
89.13 % |
231088363 |
91.92 % |
1320125 |
14.11 % |
| q20,qd2 |
11639014 |
4.46 % |
4495006 |
1.79 % |
7144008 |
76.36 % |
| q20,mq40 |
9056243 |
3.47 % |
8951597 |
3.56 % |
104646 |
1.12 % |
| qd2 |
2728852 |
1.05 % |
2361026 |
0.94 % |
367826 |
3.93 % |
| mq40 |
2461671 |
0.94 % |
2209937 |
0.88 % |
251734 |
2.69 % |
| q20,qd2,mq40 |
2403869 |
0.92 % |
2252023 |
0.90 % |
151846 |
1.62 % |
| qd2,mq40 |
63316 |
0.02 % |
50726 |
0.02 % |
12590 |
0.13 % |
| qd2,fs60,mq40 |
983 |
0.00 % |
0 |
0.00 % |
983 |
0.01 % |
| qd2,fs60 |
746 |
0.00 % |
0 |
0.00 % |
746 |
0.01 % |
| fs60 |
518 |
0.00 % |
0 |
0.00 % |
518 |
0.01 % |
| fs60,mq40 |
297 |
0.00 % |
0 |
0.00 % |
297 |
0.00 % |
| q20,qd2,fs60 |
156 |
0.00 % |
0 |
0.00 % |
156 |
0.00 % |
| q20,qd2,fs60,mq40 |
76 |
0.00 % |
0 |
0.00 % |
76 |
0.00 % |
| q20,fs60,mq40 |
2 |
0.00 % |
0 |
0.00 % |
2 |
0.00 % |
| q20,fs60 |
1 |
0.00 % |
0 |
0.00 % |
1 |
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 |
6119587 |
36.03 % |
| Transition |
G>A |
All |
992819 |
5.85 % |
| Transition |
T>C |
All |
5702513 |
33.57 % |
| Transition |
C>T |
All |
1015480 |
5.98 % |
| Transversion |
A>C |
All |
302715 |
1.78 % |
| Transversion |
C>A |
All |
566879 |
3.34 % |
| Transversion |
T>G |
All |
319376 |
1.88 % |
| Transversion |
G>T |
All |
551880 |
3.25 % |
| Transversion |
A>T |
All |
374896 |
2.21 % |
| Transversion |
T>A |
All |
387457 |
2.28 % |
| Transversion |
C>G |
All |
334384 |
1.97 % |
| Transversion |
G>C |
All |
317770 |
1.87 % |
| |
|
|
|
|
| Transition |
A>G |
Passed |
774339 |
19.60 % |
| Transition |
G>A |
Passed |
564858 |
14.30 % |
| Transition |
T>C |
Passed |
756399 |
19.14 % |
| Transition |
C>T |
Passed |
567657 |
14.37 % |
| Transversion |
A>C |
Passed |
164289 |
4.16 % |
| Transversion |
C>A |
Passed |
170601 |
4.32 % |
| Transversion |
T>G |
Passed |
166042 |
4.20 % |
| Transversion |
G>T |
Passed |
165995 |
4.20 % |
| Transversion |
A>T |
Passed |
151397 |
3.83 % |
| Transversion |
T>A |
Passed |
152413 |
3.86 % |
| Transversion |
C>G |
Passed |
159074 |
4.03 % |
| Transversion |
G>C |
Passed |
158288 |
4.01 % |
| |
|
|
|
|
| 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 |
4.38 |
13830399 |
3155357 |
| Passed |
2.07 |
2663253 |
1288099 |
| dbSNPAll |
0 |
0 |
0 |
| dbSNPPassed |
0 |
0 |
0 |