HMMCopy Reads

|Column|Description| |——|———–| |chr|chromosome| |start|start position| |end|end position| |width|width of genomie segment that comprises the bin| |reads|number of reads that start in the bin| |gc|average GC content of all bases in the bin, -1 if N is present| |map|average mappability value of bin| |cor_gc|gc-corrected copy number value| |copy|final output copy number value| |valid|TRUE if reads > 0 & gc > 0, else FALSE| |ideal|TRUE if bin is VALID with good mappability and non-outlier gc and read values| |modal_curve|value of the gc-correction modal curve given the bin’s gc| |modal_quantile|| |cor_map|mappability-corrected gc-corrected copy number value| |multiplier|hmmcopy parameter set used [1..6]| |state|the copy number state of the bin| |cell_id|label of the cell| |is_low_mappability|bool, set to True if the segment has a low mappability score|