/cemt/variants/K005728_1_lane_gembs
BACK
SAMPLE K005728_1_lane_gembs
Variant counts
| Type |
Total |
Pass |
% |
| SNPs |
1168149983 |
827222664 |
70.81 % |
| Multiallelic |
0 |
0 |
0.00 % |
VCF Filtering Stats
| Type |
#Sites |
% |
#Non-Variant Sites |
% |
#Variant Sites |
% |
| All |
1168149983 |
100% |
1150198718 |
98.46 % |
17951265 |
1.54 % |
| |
|
|
|
|
|
|
| Passed |
830962363 |
71.13 % |
824268692 |
71.66 % |
6693671 |
0.81 % |
| Filtered |
337187620 |
28.87 % |
325930026 |
28.34 % |
11257594 |
1.35 % |
| |
|
|
|
|
|
|
| q20 |
305359280 |
90.56 % |
303283891 |
93.05 % |
2075389 |
18.44 % |
| q20,qd2 |
13794780 |
4.09 % |
5550932 |
1.70 % |
8243848 |
73.23 % |
| q20,mq40 |
9776343 |
2.90 % |
9650629 |
2.96 % |
125714 |
1.12 % |
| qd2 |
3112745 |
0.92 % |
2747595 |
0.84 % |
365150 |
3.24 % |
| q20,qd2,mq40 |
2582852 |
0.77 % |
2415011 |
0.74 % |
167841 |
1.49 % |
| mq40 |
2496565 |
0.74 % |
2231805 |
0.68 % |
264760 |
2.35 % |
| qd2,mq40 |
62124 |
0.02 % |
50163 |
0.02 % |
11961 |
0.11 % |
| qd2,fs60,mq40 |
1088 |
0.00 % |
0 |
0.00 % |
1088 |
0.01 % |
| qd2,fs60 |
811 |
0.00 % |
0 |
0.00 % |
811 |
0.01 % |
| fs60 |
459 |
0.00 % |
0 |
0.00 % |
459 |
0.00 % |
| fs60,mq40 |
254 |
0.00 % |
0 |
0.00 % |
254 |
0.00 % |
| q20,qd2,fs60 |
211 |
0.00 % |
0 |
0.00 % |
211 |
0.00 % |
| q20,qd2,fs60,mq40 |
106 |
0.00 % |
0 |
0.00 % |
106 |
0.00 % |
| q20,fs60 |
1 |
0.00 % |
0 |
0.00 % |
1 |
0.00 % |
| q20,fs60,mq40 |
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 |
7102793 |
35.93 % |
| Transition |
G>A |
All |
1102472 |
5.58 % |
| Transition |
T>C |
All |
6566352 |
33.21 % |
| Transition |
C>T |
All |
1132506 |
5.73 % |
| Transversion |
A>C |
All |
370598 |
1.87 % |
| Transversion |
C>A |
All |
711555 |
3.60 % |
| Transversion |
T>G |
All |
397262 |
2.01 % |
| Transversion |
G>T |
All |
683093 |
3.46 % |
| Transversion |
A>T |
All |
429959 |
2.17 % |
| Transversion |
T>A |
All |
451067 |
2.28 % |
| Transversion |
C>G |
All |
423285 |
2.14 % |
| Transversion |
G>C |
All |
399495 |
2.02 % |
| |
|
|
|
|
| Transition |
A>G |
Passed |
799095 |
20.25 % |
| Transition |
G>A |
Passed |
548731 |
13.91 % |
| Transition |
T>C |
Passed |
786072 |
19.92 % |
| Transition |
C>T |
Passed |
552741 |
14.01 % |
| Transversion |
A>C |
Passed |
159096 |
4.03 % |
| Transversion |
C>A |
Passed |
169783 |
4.30 % |
| Transversion |
T>G |
Passed |
162105 |
4.11 % |
| Transversion |
G>T |
Passed |
162507 |
4.12 % |
| Transversion |
A>T |
Passed |
146856 |
3.72 % |
| Transversion |
T>A |
Passed |
149296 |
3.78 % |
| Transversion |
C>G |
Passed |
155391 |
3.94 % |
| Transversion |
G>C |
Passed |
153850 |
3.90 % |
| |
|
|
|
|
| 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 |
4.11 |
15904123 |
3866314 |
| Passed |
2.13 |
2686639 |
1258884 |
| dbSNPAll |
0 |
0 |
0 |
| dbSNPPassed |
0 |
0 |
0 |