/cemt/variants/A36012_3_lane_gembs
BACK
SAMPLE A36012_3_lane_gembs
Variant counts
| Type |
Total |
Pass |
% |
| SNPs |
1160122113 |
827297529 |
71.31 % |
| Multiallelic |
0 |
0 |
0.00 % |
VCF Filtering Stats
| Type |
#Sites |
% |
#Non-Variant Sites |
% |
#Variant Sites |
% |
| All |
1160122113 |
100% |
1141468586 |
98.39 % |
18653527 |
1.61 % |
| |
|
|
|
|
|
|
| Passed |
829596666 |
71.51 % |
824787700 |
72.26 % |
4808966 |
0.58 % |
| Filtered |
330525447 |
28.49 % |
316680886 |
27.74 % |
13844561 |
1.67 % |
| |
|
|
|
|
|
|
| q20 |
287438649 |
86.96 % |
284493177 |
89.84 % |
2945472 |
21.28 % |
| q20,qd2 |
20302549 |
6.14 % |
10237141 |
3.23 % |
10065408 |
72.70 % |
| q20,mq40 |
11075733 |
3.35 % |
10866236 |
3.43 % |
209497 |
1.51 % |
| qd2 |
6587325 |
1.99 % |
6377816 |
2.01 % |
209509 |
1.51 % |
| q20,qd2,mq40 |
3067289 |
0.93 % |
2837367 |
0.90 % |
229922 |
1.66 % |
| mq40 |
1981349 |
0.60 % |
1817245 |
0.57 % |
164104 |
1.19 % |
| qd2,mq40 |
61987 |
0.02 % |
51904 |
0.02 % |
10083 |
0.07 % |
| fs60 |
3575 |
0.00 % |
0 |
0.00 % |
3575 |
0.03 % |
| q20,qd2,fs60 |
3233 |
0.00 % |
0 |
0.00 % |
3233 |
0.02 % |
| qd2,fs60 |
2027 |
0.00 % |
0 |
0.00 % |
2027 |
0.01 % |
| qd2,fs60,mq40 |
1200 |
0.00 % |
0 |
0.00 % |
1200 |
0.01 % |
| fs60,mq40 |
367 |
0.00 % |
0 |
0.00 % |
367 |
0.00 % |
| q20,qd2,fs60,mq40 |
151 |
0.00 % |
0 |
0.00 % |
151 |
0.00 % |
| q20,fs60 |
12 |
0.00 % |
0 |
0.00 % |
12 |
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 |
6042232 |
29.24 % |
| Transition |
G>A |
All |
1671721 |
8.09 % |
| Transition |
T>C |
All |
5909923 |
28.60 % |
| Transition |
C>T |
All |
1674830 |
8.10 % |
| Transversion |
A>C |
All |
388314 |
1.88 % |
| Transversion |
C>A |
All |
1003859 |
4.86 % |
| Transversion |
T>G |
All |
395613 |
1.91 % |
| Transversion |
G>T |
All |
1008380 |
4.88 % |
| Transversion |
A>T |
All |
958139 |
4.64 % |
| Transversion |
T>A |
All |
961072 |
4.65 % |
| Transversion |
C>G |
All |
328345 |
1.59 % |
| Transversion |
G>C |
All |
322071 |
1.56 % |
| |
|
|
|
|
| Transition |
A>G |
Passed |
618971 |
17.68 % |
| Transition |
G>A |
Passed |
541147 |
15.46 % |
| Transition |
T>C |
Passed |
620469 |
17.72 % |
| Transition |
C>T |
Passed |
542904 |
15.51 % |
| Transversion |
A>C |
Passed |
145351 |
4.15 % |
| Transversion |
C>A |
Passed |
161717 |
4.62 % |
| Transversion |
T>G |
Passed |
146070 |
4.17 % |
| Transversion |
G>T |
Passed |
159677 |
4.56 % |
| Transversion |
A>T |
Passed |
145352 |
4.15 % |
| Transversion |
T>A |
Passed |
147404 |
4.21 % |
| Transversion |
C>G |
Passed |
135879 |
3.88 % |
| Transversion |
G>C |
Passed |
135624 |
3.87 % |
| |
|
|
|
|
| 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 |
2.85 |
15298706 |
5365793 |
| Passed |
1.97 |
2323491 |
1177074 |
| dbSNPAll |
0 |
0 |
0 |
| dbSNPPassed |
0 |
0 |
0 |