/cemt/variants/A35999_3_lane_gembs
BACK
SAMPLE A35999_3_lane_gembs
Variant counts
| Type |
Total |
Pass |
% |
| SNPs |
1166243023 |
758120292 |
65.01 % |
| Multiallelic |
0 |
0 |
0.00 % |
VCF Filtering Stats
| Type |
#Sites |
% |
#Non-Variant Sites |
% |
#Variant Sites |
% |
| All |
1166243023 |
100% |
1146041960 |
98.27 % |
20201063 |
1.73 % |
| |
|
|
|
|
|
|
| Passed |
760572974 |
65.22 % |
755762184 |
65.95 % |
4810790 |
0.63 % |
| Filtered |
405670049 |
34.78 % |
390279776 |
34.05 % |
15390273 |
2.02 % |
| |
|
|
|
|
|
|
| q20 |
357355891 |
88.09 % |
353354902 |
90.54 % |
4000989 |
26.00 % |
| q20,qd2 |
24092030 |
5.94 % |
13672276 |
3.50 % |
10419754 |
67.70 % |
| q20,mq40 |
12993541 |
3.20 % |
12710764 |
3.26 % |
282777 |
1.84 % |
| qd2 |
5257113 |
1.30 % |
5054890 |
1.30 % |
202223 |
1.31 % |
| q20,qd2,mq40 |
3453836 |
0.85 % |
3169507 |
0.81 % |
284329 |
1.85 % |
| mq40 |
2441953 |
0.60 % |
2256468 |
0.58 % |
185485 |
1.21 % |
| qd2,mq40 |
70694 |
0.02 % |
60969 |
0.02 % |
9725 |
0.06 % |
| fs60 |
1176 |
0.00 % |
0 |
0.00 % |
1176 |
0.01 % |
| qd2,fs60,mq40 |
1119 |
0.00 % |
0 |
0.00 % |
1119 |
0.01 % |
| q20,qd2,fs60 |
1117 |
0.00 % |
0 |
0.00 % |
1117 |
0.01 % |
| qd2,fs60 |
1105 |
0.00 % |
0 |
0.00 % |
1105 |
0.01 % |
| fs60,mq40 |
335 |
0.00 % |
0 |
0.00 % |
335 |
0.00 % |
| q20,qd2,fs60,mq40 |
133 |
0.00 % |
0 |
0.00 % |
133 |
0.00 % |
| q20,fs60 |
4 |
0.00 % |
0 |
0.00 % |
4 |
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 |
6452720 |
28.90 % |
| Transition |
G>A |
All |
1803698 |
8.08 % |
| Transition |
T>C |
All |
5964455 |
26.71 % |
| Transition |
C>T |
All |
1813985 |
8.12 % |
| Transversion |
A>C |
All |
496733 |
2.22 % |
| Transversion |
C>A |
All |
1104601 |
4.95 % |
| Transversion |
T>G |
All |
525030 |
2.35 % |
| Transversion |
G>T |
All |
1083720 |
4.85 % |
| Transversion |
A>T |
All |
1093475 |
4.90 % |
| Transversion |
T>A |
All |
1130442 |
5.06 % |
| Transversion |
C>G |
All |
441957 |
1.98 % |
| Transversion |
G>C |
All |
420792 |
1.88 % |
| |
|
|
|
|
| Transition |
A>G |
Passed |
593751 |
18.15 % |
| Transition |
G>A |
Passed |
499344 |
15.26 % |
| Transition |
T>C |
Passed |
582944 |
17.82 % |
| Transition |
C>T |
Passed |
502191 |
15.35 % |
| Transversion |
A>C |
Passed |
134707 |
4.12 % |
| Transversion |
C>A |
Passed |
148801 |
4.55 % |
| Transversion |
T>G |
Passed |
135730 |
4.15 % |
| Transversion |
G>T |
Passed |
148166 |
4.53 % |
| Transversion |
A>T |
Passed |
137456 |
4.20 % |
| Transversion |
T>A |
Passed |
138823 |
4.24 % |
| Transversion |
C>G |
Passed |
124635 |
3.81 % |
| Transversion |
G>C |
Passed |
125174 |
3.83 % |
| |
|
|
|
|
| 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 |
2.55 |
16034858 |
6296750 |
| Passed |
1.99 |
2178230 |
1093492 |
| dbSNPAll |
0 |
0 |
0 |
| dbSNPPassed |
0 |
0 |
0 |