/CEMT/variants/A75620_1_lane_gembs
BACK
SAMPLE A75620_1_lane_gembs
Variant counts
| Type |
Total |
Pass |
% |
| SNPs |
1178040882 |
953190408 |
80.91 % |
| Multiallelic |
0 |
0 |
0.00 % |
VCF Filtering Stats
| Type |
#Sites |
% |
#Non-Variant Sites |
% |
#Variant Sites |
% |
| All |
1178040882 |
100% |
1158461940 |
98.34 % |
19578942 |
1.66 % |
| |
|
|
|
|
|
|
| Passed |
956237425 |
81.17 % |
950020903 |
82.01 % |
6216522 |
0.65 % |
| Filtered |
221803457 |
18.83 % |
208441037 |
17.99 % |
13362420 |
1.40 % |
| |
|
|
|
|
|
|
| q20 |
186690496 |
84.17 % |
185223491 |
88.86 % |
1467005 |
10.98 % |
| q20,qd2 |
15234350 |
6.87 % |
4390354 |
2.11 % |
10843996 |
81.15 % |
| q20,mq40 |
12023567 |
5.42 % |
11881143 |
5.70 % |
142424 |
1.07 % |
| q20,qd2,mq40 |
2907630 |
1.31 % |
2739809 |
1.31 % |
167821 |
1.26 % |
| mq40 |
2565038 |
1.16 % |
2288139 |
1.10 % |
276899 |
2.07 % |
| qd2 |
2332501 |
1.05 % |
1878938 |
0.90 % |
453563 |
3.39 % |
| qd2,mq40 |
48296 |
0.02 % |
39163 |
0.02 % |
9133 |
0.07 % |
| qd2,fs60,mq40 |
651 |
0.00 % |
0 |
0.00 % |
651 |
0.00 % |
| qd2,fs60 |
323 |
0.00 % |
0 |
0.00 % |
323 |
0.00 % |
| fs60,mq40 |
235 |
0.00 % |
0 |
0.00 % |
235 |
0.00 % |
| fs60 |
228 |
0.00 % |
0 |
0.00 % |
228 |
0.00 % |
| q20,qd2,fs60 |
83 |
0.00 % |
0 |
0.00 % |
83 |
0.00 % |
| q20,qd2,fs60,mq40 |
59 |
0.00 % |
0 |
0.00 % |
59 |
0.00 % |
| q20,fs60 |
0 |
0.00 % |
0 |
0.00 % |
0 |
0.00 % |
| q20,fs60,mq40 |
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 |
7788242 |
36.50 % |
| Transition |
G>A |
All |
969949 |
4.55 % |
| Transition |
T>C |
All |
7831943 |
36.71 % |
| Transition |
C>T |
All |
975166 |
4.57 % |
| Transversion |
A>C |
All |
417373 |
1.96 % |
| Transversion |
C>A |
All |
556752 |
2.61 % |
| Transversion |
T>G |
All |
424420 |
1.99 % |
| Transversion |
G>T |
All |
539072 |
2.53 % |
| Transversion |
A>T |
All |
511277 |
2.40 % |
| Transversion |
T>A |
All |
529391 |
2.48 % |
| Transversion |
C>G |
All |
399410 |
1.87 % |
| Transversion |
G>C |
All |
393021 |
1.84 % |
| |
|
|
|
|
| Transition |
A>G |
Passed |
955969 |
22.29 % |
| Transition |
G>A |
Passed |
573006 |
13.36 % |
| Transition |
T>C |
Passed |
857600 |
19.99 % |
| Transition |
C>T |
Passed |
571803 |
13.33 % |
| Transversion |
A>C |
Passed |
174430 |
4.07 % |
| Transversion |
C>A |
Passed |
180305 |
4.20 % |
| Transversion |
T>G |
Passed |
176580 |
4.12 % |
| Transversion |
G>T |
Passed |
167899 |
3.91 % |
| Transversion |
A>T |
Passed |
147519 |
3.44 % |
| Transversion |
T>A |
Passed |
153219 |
3.57 % |
| Transversion |
C>G |
Passed |
166250 |
3.88 % |
| Transversion |
G>C |
Passed |
164820 |
3.84 % |
| |
|
|
|
|
| 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 |
4.66 |
17565300 |
3770716 |
| Passed |
2.22 |
2958378 |
1331022 |
| dbSNPAll |
0 |
0 |
0 |
| dbSNPPassed |
0 |
0 |
0 |