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.