What does solid lines on IGV mean? Mutations are noted as short line with length of 1 bp usually. But there are some solid long color lines. What do these mean?
Probably you are visualizing Insertion or deletion events .
In a gapped alignment, IGV indicates insertions with respect to the reference with a purple or red I for insertions greater than a user activated and specified cutoff
In a gapped read, IGV indicates deletions with respect to the reference with a black bar.
More details at http://www.broadinstitute.org/igv/AlignmentData
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version 2.3.6
Unlikely it is insertion or deletion. The start or end point of the solid line is at the end of sequence or fragment.
may be I was wrong. It might be insertion or deletion.