Figure 4

Intron conservation ratio (ICR) histograms in four concordant and discordant cases between Inparanoid orthology and local synteny based orthology. 7.0% of disagreement between Inparanoid orthology and local synteny based orthology and the majority (93%) of sample pairs are concordant between two orthology methods. Most of the pairs concordant between local synteny and Inparanoid, (a) syntenic Inparanoid ortholog (denoted as LS(+)/Inp(+) ) and (d) non-syntenic non-Inparanoid pairs ( LS(-)/Inp(-) ), are also concordant with ICR: orthologs have a high ICR and non-orthologs have a low ICR. However in discordant cases, (b) syntenic non-Inparanoid ( LS(+)/Inp(-) ) and (c) non-syntenic Inparanoid orthologs ( LS(-)/Inp(+) ), ICR histograms show a partial agreement with two orthology definitions. Also there are small numbers of non-syntenic non-Inparanoid pairs ( LS(-)/Inp(-) ) having perfect ICR in panel (d).