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Can Scaffolds overlap?
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13 months ago
beausoleilmo • 230
McGill University

I was wondering if Scaffolds could overlap and why.

Here is a table showing my scaffolds (Under CHR). The minPos is the minimum position of a SNP in that Scaffold and maxPos is the same thing but for the maximum. I thought that the SNPs would be positioned in non overlapping scaffolds, but now I don't understand why some of the scaffolds are overlapping.

     CHR   minPos      maxPos
1  739908   809  8420455
2  739893   981 16982050
3  740134  1196   806099
4  739934  2164  5673875
5  740027  3038  1882819
6  739900  3652 12059715
7  740035  5243  1752428
8  739891  5666 19027684
9  740062  5748  1391297
10 739970  8065  3377070
11 740050 12528  1511536
12 739951 16014  4263239
13 739890 16652 19779756

In this image, you can see that scaffolds are not overlapping. Is this a misconception of the scaffolds?

enter image description here

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I'm not really clear on your question. The diagram clearly indicates that contigs do not overlap (which is correct), and indicates that multiple contigs can be placed on the same scaffold (which is also correct). But I don't understand how this relates to the data you posted. Can you explain the meaning of the columns? You only have 3 labels for 4 columns, and it is not at all clear what any of the headers mean.

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I finally understood that a scaffold is always starting at position 1. So scaffold1 starts at 1 and ends at 500 for example. Scaffold2 could start at 1 and end at 340. I thought they were positioned relative to the "real" physical position on the genome.

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