/CEMT/variants/A34002_3_lane_gembs
BACK
SAMPLE A34002_3_lane_gembs
Variant counts
| Type |
Total |
Pass |
% |
| SNPs |
1154745809 |
878158202 |
76.05 % |
| Multiallelic |
0 |
0 |
0.00 % |
VCF Filtering Stats
| Type |
#Sites |
% |
#Non-Variant Sites |
% |
#Variant Sites |
% |
| All |
1154745809 |
100% |
1135942924 |
98.37 % |
18802885 |
1.63 % |
| |
|
|
|
|
|
|
| Passed |
880815420 |
76.28 % |
875796327 |
77.10 % |
5019093 |
0.57 % |
| Filtered |
273930389 |
23.72 % |
260146597 |
22.90 % |
13783792 |
1.56 % |
| |
|
|
|
|
|
|
| q20 |
236054019 |
86.17 % |
234619123 |
90.19 % |
1434896 |
10.41 % |
| q20,qd2 |
16153356 |
5.90 % |
4380140 |
1.68 % |
11773216 |
85.41 % |
| q20,mq40 |
14915425 |
5.44 % |
14827202 |
5.70 % |
88223 |
0.64 % |
| mq40 |
3050996 |
1.11 % |
2842208 |
1.09 % |
208788 |
1.51 % |
| q20,qd2,mq40 |
2946210 |
1.08 % |
2814327 |
1.08 % |
131883 |
0.96 % |
| qd2 |
769786 |
0.28 % |
631926 |
0.24 % |
137860 |
1.00 % |
| qd2,mq40 |
39059 |
0.01 % |
31671 |
0.01 % |
7388 |
0.05 % |
| qd2,fs60,mq40 |
755 |
0.00 % |
0 |
0.00 % |
755 |
0.01 % |
| fs60,mq40 |
402 |
0.00 % |
0 |
0.00 % |
402 |
0.00 % |
| qd2,fs60 |
167 |
0.00 % |
0 |
0.00 % |
167 |
0.00 % |
| q20,qd2,fs60,mq40 |
111 |
0.00 % |
0 |
0.00 % |
111 |
0.00 % |
| fs60 |
74 |
0.00 % |
0 |
0.00 % |
74 |
0.00 % |
| q20,qd2,fs60 |
28 |
0.00 % |
0 |
0.00 % |
28 |
0.00 % |
| q20,fs60,mq40 |
1 |
0.00 % |
0 |
0.00 % |
1 |
0.00 % |
| q20,fs60 |
0 |
0.00 % |
0 |
0.00 % |
0 |
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 |
8092455 |
39.61 % |
| Transition |
G>A |
All |
938102 |
4.59 % |
| Transition |
T>C |
All |
7941425 |
38.87 % |
| Transition |
C>T |
All |
934374 |
4.57 % |
| Transversion |
A>C |
All |
210549 |
1.03 % |
| Transversion |
C>A |
All |
459100 |
2.25 % |
| Transversion |
T>G |
All |
212324 |
1.04 % |
| Transversion |
G>T |
All |
449530 |
2.20 % |
| Transversion |
A>T |
All |
391420 |
1.92 % |
| Transversion |
T>A |
All |
389032 |
1.90 % |
| Transversion |
C>G |
All |
206398 |
1.01 % |
| Transversion |
G>C |
All |
205208 |
1.00 % |
| |
|
|
|
|
| Transition |
A>G |
Passed |
611348 |
18.27 % |
| Transition |
G>A |
Passed |
517989 |
15.48 % |
| Transition |
T>C |
Passed |
610760 |
18.25 % |
| Transition |
C>T |
Passed |
521401 |
15.58 % |
| Transversion |
A>C |
Passed |
136255 |
4.07 % |
| Transversion |
C>A |
Passed |
143514 |
4.29 % |
| Transversion |
T>G |
Passed |
136387 |
4.07 % |
| Transversion |
G>T |
Passed |
143705 |
4.29 % |
| Transversion |
A>T |
Passed |
127535 |
3.81 % |
| Transversion |
T>A |
Passed |
127878 |
3.82 % |
| Transversion |
C>G |
Passed |
134693 |
4.02 % |
| Transversion |
G>C |
Passed |
135485 |
4.05 % |
| |
|
|
|
|
| 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 |
7.10 |
17906356 |
2523561 |
| Passed |
2.08 |
2261498 |
1085452 |
| dbSNPAll |
0 |
0 |
0 |
| dbSNPPassed |
0 |
0 |
0 |