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			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.
			 
			Example:
			  fill 58159 3681 chr7 + 17527587 9297 id 43830 score 143688 qDup 8727 
	type top tN 0 qN 0 tR 309 qR 345 tNewR 309 qNewR 246 tOldR 0 qOldR 0 tTrf 29 qTrf 0
  gap 59899 104 chr7 + 17531210 4178 tN 0 qN 0 tR 0 qR 246 tNewR 0 qNewR 246 tOldR 0 qOldR 0 
  	tTrf 0 qTrf 0
  gap 60324 117 chr7 + 17535966 0 tN 0 qN 0 tR 0 qR 0 tNewR 0 qNewR 0 tOldR 0 qOldR 0 
	tTrf 0 qTrf 0
  fill 60325 101 chr7 + 17536081 101 id 5137619 score 6111 qOver 0 qFar 115 qDup 101 
	type syn tN 0 qN 0 tR 0 qR 0 tNewR 0 qNewR 0 tOldR 0 qOldR 0 tTrf 0 qTrf 0
  gap 60558 106 chr7 + 17536066 0 tN 0 qN 0 tR 0 qR 0 tNewR 0 qNewR 0 tOldR 0 qOldR 0 
	tTrf 0 qTrf 0
  fill 60558 106 chr7 - 17531782 4202 id 1670092 score 15263 qOver 0 qFar 82 qDup 4202 
	type inv tN 0 qN 0 tR 0 qR 246 tNewR 0 qNewR 246 tOldR 0 qOldR 0 tTrf 0 qTrf 0
  gap 60671 63 chr7 + 17536073 0 tN 0 qN 0 tR 0 qR 0 tNewR 0 qNewR 0 tOldR 0 qOldR 0 
	tTrf 0 qTrf 0
  fill 60671 26 chr7 - 17531815 26 id 1670092 score 15263 qOver 0 qFar 4232 qDup 26 
	type inv tN 0 qN 0 tR 0 qR 0 tNewR 0 qNewR 0 tOldR 0 qOldR 0 tTrf 0 qTrf 0
  gap 61069 320 chr7 + 17536433 0 tN 0 qN 0 tR 309 qR 0 tNewR 309 qNewR 0 tOldR 0 qOldR 0 
	tTrf 29 qTrf 0 
			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.
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