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After a close inspection, the assembly does look pretty janky.
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Upon manual inspection of the assembly, we identified some mRNA species that were assembled as multiple contigs because of sequencing errors.
Ford said the problem was discovered late in November during an inspection at the assembly plant.
Chrysler said a routine inspection at the assembly plant revealed that an incorrect sensing system had been installed.
Volkswagen said it became aware of a problem during a "routine production inspection" at the assembly plant in Mexico in June.
However, a close inspection of the assembly of 454 sequences resulted in a high number of discrepancies from the KIM 10+ reference genome, including SNPs and INDELs (Figure 1).
The open reading frame of 48 genes could be restored by manual inspection of the assembly alignments.
Contigs containing suspected sequencing errors (mainly insertions/deletions in homopolymer regions) were edited manually after identifying miss-assemblies through manual inspection of the assembly files, ESTs, or genomic data (D. ponderosae) [ 63].
The manual inspection of the assembly confirmed that there was evidence (multiple high quality reads) supporting all 10 of the predicted photoprotein genes, therefore confirming 10 out of 10 full-length genes.
A closer inspection of the assemblies indicates that GAML missed several possible joins.
An inspection of the assemblies does reveal several patterns of polymorphisms that might arise from homoeologues, but the sequencing depth is not adequate for any conclusions to be drawn.
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