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Fosmid contamination in C. elegans genome?

In the C. elegans chromosome X (NC_003284.9) is a complete copy of the C. elegans fosmid H05L03 (FO081428.1) at positions 5898291-5912640. I understand fosmids are vectors used to build sequencing libraries, so is this a contamination?

genome
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updated by Ahill Ahill • written by gtrwst9 • gtrwst9

1 answer

The chromsome X sequence was assembled from genomic DNA fragments that were packaged into fosmids. In this case, your fosmid (FO081428.1) was one of a number of fosmids that were assembled together to form the inferred chromosome X sequence (NC_003284.9). So this is not a contamination - in fact the chr X sequence was literally assembled from many individual fosmid insert sequences. See the contig entry in the chr X genbank record here.

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written by Ahill Ahill

While it is ok for the genomic sequence to match an fosmid sequence entry, if any functional element sequences from fosmid are present in the genome assembly then that is contamination. gtrwst9 : You would want to check to see if that is the case.

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written by GenoMax GenoMax

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