Tag processing. (a) Tags mapping to a hypothetical gene model, definition of terms. Sense tags were defined to be those tags on the same strand as the gene model, antisense tags were on the opposite strand. The 'On 3' terminus' tags were defined to be on the 3' terminus derived from the two downstream-most positions on the transcript, while the rest of the tags within the gene boundaries were defined to be 'Not on 3' terminus'. The union of these two sets was defined as tags 'Within locus'. (b) Tag genome mapping and filtering. The ordinate 'Total normalized tag abundance' is the sum of all normalized tag counts (TPM) over all tissues, while the abscissa 'Number of unique tag sequences' is the set of tags from all 95 tissues. Os, operative set of all observed tags that do not possess an ambiguous base; Os-G, subset of Os tags perfectly mapping to the draft bovine genome; Os-F, subset of Os tags found in at least ten tissues and/or have a tag abundance of 2 TPM or greater in at least one tissue; Os-fG, subset of Os-F tags that mapped to the draft bovine genome; Os-fgU, subset of Os-fG tags with unique matches to the draft bovine genome - the Os-fgU tag set is analyzed further in Additional file 1 and is marked with a concentric circle; OS-fgu-PC, the subset of Os-fgU tags mapping to protein-coding genes; OS-fNG, the subset of Os-F tags that do not map to the draft bovine genome; OS-fng-SMM, the subset of Os-fNG tags that map back to the draft genome because of a single base mismatch at tag base positions 5 to 20; Os-fng-EST, subset of the Os-fNG tags that map to bovine ESTs.