Alignments to the human genome (NCBI 36 - Ensembl 42) were run using Illumina's (Solexa) alignment program called Eland
The output of the resulting alignment files is as follows:
  
1. Sequence name (derived from file name and line number if format is not Fasta)
2. Sequence
3. Type of match:
	NM - no match found.
	QC - no matching done: QC failure (too many Ns basically).
	RM - no matching done: repeat masked (may be seen if repeatFile.txt was specified).
	U0 - Best match found was a unique exact match.
	U1 - Best match found was a unique 1-error match.
	U2 - Best match found was a unique 2-error match.
	R0 - Multiple exact matches found.
	R1 - Multiple 1-error matches found, no exact matches.
	R2 - Multiple 2-error matches found, no exact or 1-error matches.
4. Number of exact matches found.
5. Number of 1-error matches found.
6. Number of 2-error matches found.
	Rest of fields are only seen if a unique best match was found (i.e. the match code in field 3 begins with "U").
7. Genome file in which match was found.
8. Position of match (bases in file are numbered starting at 1).
9. Direction of match (F=forward strand, R=reverse).
10. How N characters in read were interpreted: ("."=not applicable, "D"=deletion, "I"=insertion).
	Rest of fields are only seen in the case of a unique inexact match (i.e. the match code was U1 or U2).
11. Position and type of first substitution error (e.g. 12A: base 12 was A, not whatever is was in read).
12. Position and type of first substitution error, as above.