column	description
total number of reads	Total number of reads obtained
total number of used reads	Total number of reads used for the alignemnt
mapped reads	Number of reads that mapped to either the genome or junction reference database
genome mapped reads	Mapped Genome Reads and percentage (Mapped Genome Reads/Total number of reads)
junction mapped reads	Mapped Jucntion Reads and percentage (Mapped Junction Reads/ Total number of reads)
gene counts	Number of base-pairs of sequencing data mapping to the exon regions of UCSC annotated genes from the refFlat file.
exon counts	Number of base-pairs of sequencing data mapping to the exon regions of UCSC annotated genes from the refFlat file. May contain redundant counts due to overlapping exons.