/cemt/variants/A70095_3_lane_gembs
BACK
SAMPLE A70095_3_lane_gembs
Variant counts
| Type |
Total |
Pass |
% |
| SNPs |
1168981588 |
1082923675 |
92.64 % |
| Multiallelic |
0 |
0 |
0.00 % |
VCF Filtering Stats
| Type |
#Sites |
% |
#Non-Variant Sites |
% |
#Variant Sites |
% |
| All |
1168981588 |
100% |
1152996687 |
98.63 % |
15984901 |
1.37 % |
| |
|
|
|
|
|
|
| Passed |
1084219668 |
92.75 % |
1079841951 |
93.66 % |
4377717 |
0.40 % |
| Filtered |
84761920 |
7.25 % |
73154736 |
6.34 % |
11607184 |
1.07 % |
| |
|
|
|
|
|
|
| q20 |
54411091 |
64.19 % |
53871985 |
73.64 % |
539106 |
4.64 % |
| q20,qd2 |
12976271 |
15.31 % |
2869487 |
3.92 % |
10106784 |
87.07 % |
| q20,mq40 |
10081637 |
11.89 % |
9978381 |
13.64 % |
103256 |
0.89 % |
| mq40 |
2972997 |
3.51 % |
2721262 |
3.72 % |
251735 |
2.17 % |
| q20,qd2,mq40 |
2424188 |
2.86 % |
2275537 |
3.11 % |
148651 |
1.28 % |
| qd2 |
1842926 |
2.17 % |
1397819 |
1.91 % |
445107 |
3.83 % |
| qd2,mq40 |
51071 |
0.06 % |
40265 |
0.06 % |
10806 |
0.09 % |
| qd2,fs60,mq40 |
780 |
0.00 % |
0 |
0.00 % |
780 |
0.01 % |
| qd2,fs60 |
337 |
0.00 % |
0 |
0.00 % |
337 |
0.00 % |
| fs60,mq40 |
300 |
0.00 % |
0 |
0.00 % |
300 |
0.00 % |
| fs60 |
232 |
0.00 % |
0 |
0.00 % |
232 |
0.00 % |
| q20,qd2,fs60,mq40 |
45 |
0.00 % |
0 |
0.00 % |
45 |
0.00 % |
| q20,qd2,fs60 |
44 |
0.00 % |
0 |
0.00 % |
44 |
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 |
6433261 |
36.42 % |
| Transition |
G>A |
All |
929523 |
5.26 % |
| Transition |
T>C |
All |
6520013 |
36.91 % |
| Transition |
C>T |
All |
937126 |
5.31 % |
| Transversion |
A>C |
All |
266357 |
1.51 % |
| Transversion |
C>A |
All |
441739 |
2.50 % |
| Transversion |
T>G |
All |
271631 |
1.54 % |
| Transversion |
G>T |
All |
428597 |
2.43 % |
| Transversion |
A>T |
All |
466010 |
2.64 % |
| Transversion |
T>A |
All |
478759 |
2.71 % |
| Transversion |
C>G |
All |
246025 |
1.39 % |
| Transversion |
G>C |
All |
243861 |
1.38 % |
| |
|
|
|
|
| Transition |
A>G |
Passed |
872265 |
20.09 % |
| Transition |
G>A |
Passed |
631837 |
14.55 % |
| Transition |
T>C |
Passed |
845567 |
19.47 % |
| Transition |
C>T |
Passed |
633808 |
14.60 % |
| Transversion |
A>C |
Passed |
174130 |
4.01 % |
| Transversion |
C>A |
Passed |
181216 |
4.17 % |
| Transversion |
T>G |
Passed |
175311 |
4.04 % |
| Transversion |
G>T |
Passed |
173180 |
3.99 % |
| Transversion |
A>T |
Passed |
154679 |
3.56 % |
| Transversion |
T>A |
Passed |
157799 |
3.63 % |
| Transversion |
C>G |
Passed |
170863 |
3.94 % |
| Transversion |
G>C |
Passed |
171261 |
3.94 % |
| |
|
|
|
|
| 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 |
5.21 |
14819923 |
2842979 |
| Passed |
2.20 |
2983477 |
1358439 |
| dbSNPAll |
0 |
0 |
0 |
| dbSNPPassed |
0 |
0 |
0 |