/cemt/variants/A54773_3_lane_gembs
BACK
SAMPLE A54773_3_lane_gembs
Variant counts
| Type |
Total |
Pass |
% |
| SNPs |
1170091345 |
684391091 |
58.49 % |
| Multiallelic |
0 |
0 |
0.00 % |
VCF Filtering Stats
| Type |
#Sites |
% |
#Non-Variant Sites |
% |
#Variant Sites |
% |
| All |
1170091345 |
100% |
1145216676 |
97.87 % |
24874669 |
2.13 % |
| |
|
|
|
|
|
|
| Passed |
688197607 |
58.82 % |
682156056 |
59.57 % |
6041551 |
0.88 % |
| Filtered |
481893738 |
41.18 % |
463060620 |
40.43 % |
18833118 |
2.74 % |
| |
|
|
|
|
|
|
| q20 |
428133019 |
88.84 % |
422948888 |
91.34 % |
5184131 |
27.53 % |
| q20,qd2 |
26379619 |
5.47 % |
13617781 |
2.94 % |
12761838 |
67.76 % |
| q20,mq40 |
11667523 |
2.42 % |
11446422 |
2.47 % |
221101 |
1.17 % |
| qd2 |
10448482 |
2.17 % |
10224693 |
2.21 % |
223789 |
1.19 % |
| q20,qd2,mq40 |
3458172 |
0.72 % |
3224192 |
0.70 % |
233980 |
1.24 % |
| mq40 |
1718064 |
0.36 % |
1535025 |
0.33 % |
183039 |
0.97 % |
| qd2,mq40 |
75140 |
0.02 % |
63619 |
0.01 % |
11521 |
0.06 % |
| q20,qd2,fs60 |
4072 |
0.00 % |
0 |
0.00 % |
4072 |
0.02 % |
| qd2,fs60 |
3708 |
0.00 % |
0 |
0.00 % |
3708 |
0.02 % |
| fs60 |
3702 |
0.00 % |
0 |
0.00 % |
3702 |
0.02 % |
| qd2,fs60,mq40 |
1527 |
0.00 % |
0 |
0.00 % |
1527 |
0.01 % |
| fs60,mq40 |
491 |
0.00 % |
0 |
0.00 % |
491 |
0.00 % |
| q20,qd2,fs60,mq40 |
210 |
0.00 % |
0 |
0.00 % |
210 |
0.00 % |
| q20,fs60 |
7 |
0.00 % |
0 |
0.00 % |
7 |
0.00 % |
| q20,fs60,mq40 |
2 |
0.00 % |
0 |
0.00 % |
2 |
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 |
9281170 |
33.72 % |
| Transition |
G>A |
All |
2107913 |
7.66 % |
| Transition |
T>C |
All |
6893451 |
25.04 % |
| Transition |
C>T |
All |
2279251 |
8.28 % |
| Transversion |
A>C |
All |
453278 |
1.65 % |
| Transversion |
C>A |
All |
1323875 |
4.81 % |
| Transversion |
T>G |
All |
580447 |
2.11 % |
| Transversion |
G>T |
All |
1236182 |
4.49 % |
| Transversion |
A>T |
All |
1181303 |
4.29 % |
| Transversion |
T>A |
All |
1273458 |
4.63 % |
| Transversion |
C>G |
All |
520490 |
1.89 % |
| Transversion |
G>C |
All |
394625 |
1.43 % |
| |
|
|
|
|
| Transition |
A>G |
Passed |
642798 |
20.43 % |
| Transition |
G>A |
Passed |
460249 |
14.63 % |
| Transition |
T>C |
Passed |
551167 |
17.52 % |
| Transition |
C>T |
Passed |
466327 |
14.82 % |
| Transversion |
A>C |
Passed |
124825 |
3.97 % |
| Transversion |
C>A |
Passed |
138838 |
4.41 % |
| Transversion |
T>G |
Passed |
129763 |
4.12 % |
| Transversion |
G>T |
Passed |
138186 |
4.39 % |
| Transversion |
A>T |
Passed |
125025 |
3.97 % |
| Transversion |
T>A |
Passed |
126512 |
4.02 % |
| Transversion |
C>G |
Passed |
122849 |
3.90 % |
| Transversion |
G>C |
Passed |
119692 |
3.80 % |
| |
|
|
|
|
| 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 |
2.95 |
20561785 |
6963658 |
| Passed |
2.07 |
2120541 |
1025690 |
| dbSNPAll |
0 |
0 |
0 |
| dbSNPPassed |
0 |
0 |
0 |