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  • IGV Green and Red reads at same locus.

    Hello,
    I am viewing bam files in IGV and have a question. These bam files are generated from whole genome paired-end sequencing performed on human genomic DNA using Illumina instrument.

    Attached IGV screenshot shows bam files aligned to human reference genome, alignment viewed as "pairs" and alignment colored by "insert size and pair orientation". As far as I know, green colored reads are indicative of tandem duplication whereas red colored reads are indicative of a deletion. But I don't know what it means when both red and green reads are present at the same genomic location (as shown in the attached screenshot)? Can anyone please help me understand this? Thanks!
    Attached Files

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