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  • A question about alignment depth

    What is the definition of 'alignment depth', it seems it is also called 'reads depth'? what information can be acquired from 'alignment depth'?

    Thanks.

  • #2
    Essentially, it boils down to how many times each sequenced base is covered. The more depth, the more confidence you gain in your data.

    At the most basic level, most organisms I've worked with are diploid, so you get information about the SNPs present in the alleles (eg, homozygous or heterozygous.) I've seen various presentations where people have claimed that upwards of 50x coverage is required to truly required to really know if you have heterozygous SNPs, though what the minimum dept required really is depends on the technology and the method used to call SNPs.

    There are always inherent errors in the wet lab as well as the dry lab portions of any experiment. The more depth you get, the more support you get for your observations.

    Does that help?
    Last edited by apfejes; 01-14-2009, 09:04 AM. Reason: typo & clarity
    The more you know, the more you know you don't know. —Aristotle

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    • #3
      So helpful.
      Thanks million.

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      • #4
        What is the difference between depth and coverage?
        When someone says that obtained 50X average coverage for a specific window, does this mean the depth?

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        • #5
          Strictly speaking, I think they're exactly the same, but people often use them in different contexts, particularly with haploid/diploid organisms.

          When talking about a window, you can probably use them interchangeably.

          When talking about sequencing a SNP in a diploid organism, it's possible that you observe the SNP on one one half of the reads that map to a given point in the reference genome. Thus, you might have a depth of 50 at that point (50 reads cover that location), but the SNP itself has a coverage of 25X. (only half of the reads at that location have the SNP.)

          I'm sure there are people who will use them in the opposite manner as well.
          The more you know, the more you know you don't know. —Aristotle

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          • #6
            Ok, thank you for the reply! It makes sense

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