Table 3.
Validation of assembled contigs by re-sequencing using Sanger technology
|
ContigID |
Best blastx |
ORF complete? |
Frameshifts |
Contig length, bp |
Checked by Sanger |
Insertions |
Deletions |
Substitutions |
% Discrepancy |
|---|---|---|---|---|---|---|---|---|---|
| match | in ORF | sequencing, bp | |||||||
| Contig3756 |
CENPS |
yes |
no |
665 |
564 |
8 |
0 |
1 |
1.60% |
| Contig7869 |
Myc |
yes |
no |
3,268 |
2,922 |
0 |
0 |
0 |
0.00% |
| Contig54848 |
HuD/Elav |
yes |
1 |
4,404 |
3,431 |
9 |
2 |
3 |
0.41% |
| Contig19303 |
Lgr5 |
both 5’ and 3’ ends are missing |
no |
1,510 |
1,510 |
0 |
0 |
0 |
0.00% |
| Contig40997 |
NeuroD |
both 5’ and 3’ ends are missing |
no |
745 |
470 |
0 |
1 |
2 |
0.64% |
| Contig1064 |
NF1A |
yes |
no |
5,279 |
3,825 |
3 |
9 |
1 |
0.34% |
| Contig32193 |
NvProtien1 |
5’ end is missing |
no |
2,411 |
1,986 |
0 |
1 |
0 |
0.05% |
| Contig51632 |
Oct |
both 5’ and 3’ ends are missing |
no |
1,947 |
1947 |
0 |
0 |
0 |
0.00% |
| Contig46302 |
Piwi |
yes |
no |
3,430 |
2,929 |
0 |
0 |
3 |
0.10% |
| Contig67140 |
Sox |
yes |
no |
3,096 |
2,889 |
2 |
0 |
0 |
0.07% |
| Contig20197 |
unknown |
NA |
NA |
1,339 |
1,252 |
2 |
0 |
0 |
0.16% |
| Contig68289 |
Wnt3 |
yes |
no |
2,561 |
990 |
2 |
0 |
2 |
0.40% |
| Contig50192 |
DCLK |
yes |
no |
3,152 |
2,474 |
0 |
0 |
3 |
0.12% |
| Contig8186 |
Lhx |
yes |
no |
5,430 |
3,041 |
0 |
0 |
5 |
0.16% |
| Contig3071 |
FoxJ1 |
yes |
no |
2,523 |
2,404 |
2 |
3 |
0 |
0.21% |
| Contig10179 |
Klf |
yes |
no |
2,336 |
2,074 |
1 |
0 |
0 |
0.05% |
| TOTAL: | 44,096 | 34,708 | 29 | 16 | 20 | 0.19% |