NET format

The net file format is used to describe the axtNet data that underlie the net alignment annotations in the Genome Browser. For a detailed description of the methods used to generate these data, refer to the Genome Browser description pages that accompany the Net alignment tracks.   File format The net file consists of 7 fixed fields and a set of optional name/value pairs. In the descriptions below, target refers to the reference species and query refers to the aligning species. Fixed fields: Class. Either fill or gap.  Fill refers to a portion of a chain. Start in chromosome (target species) Size (target species) Chromsome name (query species) Relative orientation between target and query species. Start in chromsome (query species) Size (query species) Name/value pairs (optional): id -- ID of associated chain (gapped alignment), if any. score -- Score of associated chain. ali   -- Number of bases in alignments in chain. qFar -- For fill that is on the same chromosome as parent, how far fill is from position predicted by parent.   This helps determine if a        rearrangement is local or if a duplication is tandem. qOver -- Number of bases overlapping with parent gap on query side.  Generally, this will be near zero, except for inverts. qDup -- Number of bases in query region that are used twice or more in net. This helps distinguish between a rearrangement and a duplication. type -- One of the following values:    top -- Chain is top-level, not a gap filler    syn -- Chain is on same chromosome and in same direction as parent    inv -- Chain is on same chromosome on opposite direction from parent nonSyn -- Chain is on a different chromosome from parent tN -- Number of unsequenced bases (Ns) on target side qN -- Number of unsequenced bases on query side tR -- Number of bases in RepeatMasker masked repeats on target. qR -- Number of bases in RepeatMasker masked repeats on query. tNewR -- Bases in lineage-specific repeats on target. qNewR -- Bases in lineage-specific repeats on query. tOldR -- Bases in repeats predating split on target. qOldR -- Bases in repeats predating split on query. tTrf -- Bases in trf (Tandem Repeat Finder) repeats on target. qTrf -- Bases in trf repeats on query.