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.