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GS Mapper output to consed shows dimmed ends with good sequence?

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  • GS Mapper output to consed shows dimmed ends with good sequence?

    Somewhat serendipitously I was able to sequence a genome to 60X coverage. I used mapper to align it to a good reference sequence. The results were 6 contigs. When I opened the ace file in the consed folder to look at the folder, I noticed dimmed sequence on many individual reads overhanging the end of the contigs. Sometimes this dimmed sequence stretched for 200+ nt. It does not contribute to the consensus. It is obvious to the eye that this sequence joins contigs often with very deep coverage. The dimmed sequence is made up of lowercase and uppercase letters, and consed scores the individual bases sometimes as high as bases that contribute the consensus.

    Any ideas what these dimmed sequences represent and why they won't join or contribute to the consensus?

    1) Could they represent ghosts of trimmed sequences? The MID adaptors I use are visible at the end of the dimmed regions (and are represented as dimmed throughout).

    2) In order to join the contigs manually, I have to remove the reference sequence. Could the dimmed sequence represents large stretches that wouldn't align with the reference (ie indels)?

    Thanks for your imput.