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Old 12-22-2016, 03:38 AM   #1
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Default General IGV question about pileup

In IGV what does a variant found only in white space denote. I don't think its real but trying to figure it out. For example, in the attached all the C are located in the white space. Thank you .
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Old 12-22-2016, 05:24 AM   #2
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I'm not sure because the fill can be set via preferences to denote various characteristics of the read. But it is attractive to think that it might denote in this case a failure to map the paired read? Attractive because that would suggest that the locus has a paralog elsewhere in the genome with a slightly different sequence.

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