/CEMT/variants/B33201_1_lane_gembs
BACK
SAMPLE B33201_1_lane_gembs
Variant counts
| Type |
Total |
Pass |
% |
| SNPs |
1171032429 |
862135101 |
73.62 % |
| Multiallelic |
0 |
0 |
0.00 % |
VCF Filtering Stats
| Type |
#Sites |
% |
#Non-Variant Sites |
% |
#Variant Sites |
% |
| All |
1171032429 |
100% |
1149787804 |
98.19 % |
21244625 |
1.81 % |
| |
|
|
|
|
|
|
| Passed |
866326665 |
73.98 % |
859267608 |
74.73 % |
7059057 |
0.81 % |
| Filtered |
304705764 |
26.02 % |
290520196 |
25.27 % |
14185568 |
1.64 % |
| |
|
|
|
|
|
|
| q20 |
271922876 |
89.24 % |
269952994 |
92.92 % |
1969882 |
13.89 % |
| q20,qd2 |
16573754 |
5.44 % |
5053112 |
1.74 % |
11520642 |
81.21 % |
| q20,mq40 |
9566410 |
3.14 % |
9459843 |
3.26 % |
106567 |
0.75 % |
| q20,qd2,mq40 |
2543124 |
0.83 % |
2428766 |
0.84 % |
114358 |
0.81 % |
| qd2 |
2385638 |
0.78 % |
2135583 |
0.74 % |
250055 |
1.76 % |
| mq40 |
1662127 |
0.55 % |
1452577 |
0.50 % |
209550 |
1.48 % |
| qd2,mq40 |
45724 |
0.02 % |
37321 |
0.01 % |
8403 |
0.06 % |
| fs60 |
2130 |
0.00 % |
0 |
0.00 % |
2130 |
0.02 % |
| qd2,fs60 |
1447 |
0.00 % |
0 |
0.00 % |
1447 |
0.01 % |
| qd2,fs60,mq40 |
1187 |
0.00 % |
0 |
0.00 % |
1187 |
0.01 % |
| q20,qd2,fs60 |
996 |
0.00 % |
0 |
0.00 % |
996 |
0.01 % |
| fs60,mq40 |
264 |
0.00 % |
0 |
0.00 % |
264 |
0.00 % |
| q20,qd2,fs60,mq40 |
86 |
0.00 % |
0 |
0.00 % |
86 |
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 |
8510736 |
37.04 % |
| Transition |
G>A |
All |
1096004 |
4.77 % |
| Transition |
T>C |
All |
8497960 |
36.98 % |
| Transition |
C>T |
All |
1092711 |
4.76 % |
| Transversion |
A>C |
All |
498840 |
2.17 % |
| Transversion |
C>A |
All |
512423 |
2.23 % |
| Transversion |
T>G |
All |
505594 |
2.20 % |
| Transversion |
G>T |
All |
498517 |
2.17 % |
| Transversion |
A>T |
All |
437190 |
1.90 % |
| Transversion |
T>A |
All |
444208 |
1.93 % |
| Transversion |
C>G |
All |
444048 |
1.93 % |
| Transversion |
G>C |
All |
440955 |
1.92 % |
| |
|
|
|
|
| Transition |
A>G |
Passed |
758722 |
19.57 % |
| Transition |
G>A |
Passed |
542165 |
13.98 % |
| Transition |
T>C |
Passed |
756413 |
19.51 % |
| Transition |
C>T |
Passed |
542035 |
13.98 % |
| Transversion |
A>C |
Passed |
171187 |
4.41 % |
| Transversion |
C>A |
Passed |
172075 |
4.44 % |
| Transversion |
T>G |
Passed |
173488 |
4.47 % |
| Transversion |
G>T |
Passed |
163123 |
4.21 % |
| Transversion |
A>T |
Passed |
143144 |
3.69 % |
| Transversion |
T>A |
Passed |
145480 |
3.75 % |
| Transversion |
C>G |
Passed |
155378 |
4.01 % |
| Transversion |
G>C |
Passed |
154209 |
3.98 % |
| |
|
|
|
|
| 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 |
5.08 |
19197411 |
3781775 |
| Passed |
2.03 |
2599335 |
1278084 |
| dbSNPAll |
0 |
0 |
0 |
| dbSNPPassed |
0 |
0 |
0 |