Info on data files supporting Hardison et al. (2003) Genome Research 13:13-26

Various measures of sequence similarity and genomic properties were computed in 1 Mb non-overlapping windows (file alnAncSub_GP_1Md4redSort.txt) and in 5 Mb windows with a 1Mb slide (overlapping by 4Mb) (file alnAncSub_GP_5M(1)d4redSort.txt). This description was written in 2008 when the data were posted to our website in response to a request. It is accurate to the best recollection of Ross Hardison, please let us know if there are issues or inconsistencies. 

The data are for the June 2002 human genome assembly, as aligned to the mouse assembly of February 2002 using blastZ and processing by axtBest. See Methods for the paper for more detail.

These columns in each file are:

chr	chromosome name (number or X)
start	start position 
end	end position
sequencedBases	number of nucleotides sequenced in the window
noGapAlignedBases	number of nucleotides in the window that are included in gap-free alignments (includes mismatches)
matchingBases	number of nucleotides in the window that match with mouse
nonLSrepBases	number of nucleotides that are not in lineage-specific repeats (hence are inferred to be ancestral)
nonLSrepNoGapAlignedBases	number of nucleotides that are not in lineage-specific repeats and are in gap-free alignments
nonLSrepMatchingBases	number of nucleotides that are not in lineage-specific repeats and match with mouse
%id	percent identity of aligned nucleotides in the window
aln_tot	fraction of nucleotides in the window that align with mouse
aln_anc	fraction of nucleotides that are not lineage-specific (i.e. ancestral) in the window that align with mouse
fLSrep	fraction of nucleotides that are in lineage-specific repeats
Lsrep	number of nucleotides that are in lineage-specific repeats
fLSrep_noAlu	fraction of nucleotides that are in lineage-specific repeats but excluding Alu repeats
LSRep_noAlu	number of nucleotides that are in lineage-specific repeats but excluding Alu repeats
NA_anc	fraction of a window inferred to be ancestral that does NOT align with mouse (i.e. 1-aln_anc)
t_4d	substitutions per 4-fold degenerate site, using the REV model to estimate substitution rates
count_4d	number of 4-fold degenerate sites in each window
t_AR	substitutions per AR (ancestral repeat) site, using the REV model to estimate substitution rates
count_AR	number of AR (ancestral repeat) sites in each window
rcb	recombination rate estimated from Kong et al (2002) data
GC	percent (G+C) for each window
SNP	count of SNPs in each window
LS_L1	fraction of window occupied by lineage-specific L1 repeats
All_L1	fraction of window occupied by all L1 repeats
LS_LTR	fraction of window occupied by lineage-specific LTR repeats
All_LTR	fraction of window occupied by all LTR repeats
dGC	difference in GC content between human and mouse
CDs	fraction of window occupied by coding sequences
CpG	fraction of window occupied by CpG dinucleotides