Species Burkholderia cenocepacia J2315 Comparison species in tree Genbank assemblies used GCF_000009485.1 GCF_000203915.1 GCF_000022645.2 GCF_000013645.1 GCF_000959505.1 GCF_000198775.1 Tree ((((((B_cenocepacia, B_ambifaria)i0,B_thailandensis)i1,B_dolosa)i2, B_glumae)i3,B_xenovorans)i4,P_rhizoxinica)i5; Chromosome Start End Basewise coverage by xenoGI islands Extra Coverage Num Overlapping xenoGI islands Notes NC_011000.1 100429 124868 0.954 4.092 5 The extra coverage and multiple islands appear to be wrong NC_011000.1 188900 204338 1 0.345 1 The extra coverage appears to be legitimate NC_011000.1 449975 463085 1 0 1 NC_011000.1 1223099 1314635 1 0.07 1 NC_011000.1 1403502 1436902 0.809 0.583 1 The extra coverage appears to be legitimate NC_011000.1 1729077 1766346 1 0.014 1 NC_011000.1 2738517 2859770 1 0 1 NC_011000.1 3241751 3257931 0.828 0 1 NC_011000.1 3368967 3374914 1 2.578 1 The extra coverage appears to be legitimate NC_011001.1 290334 334228 1 1.858 1 The extra coverage appears to be legitimate NC_011001.1 1140270 1186780 1 0 1 NC_011001.1 2091958 2137530 0.974 0.047 1 NC_011002.1 573366 609590 1 23.116 1 This validation island was omitted from our analysis because it is on a pladmid. xenoGI is not well suited to analyzing plasmids. Species Corynebacterium diphtheriae NCTC 13129 Comparison species in tree Genbank assemblies used GCF_000195815.1 GCF_000833575.1 GCF_000011325.1 GCF_000525655.1 GCF_000196695.1 Tree ((((C_diphtheriae, C_singulare)i0,C_glutamicum)i1,C_falsenii)i2,R_equi)i3; Chromosome Start End Basewise coverage by xenoGI islands Extra Coverage Num overlapping xenoGI islands Notes BX248353.1 154365 190661 0.957 0.584 2 The extra coverage on the right apears legitimate, extra coverage on the left does not. BX248353.1 190816 208117 1 1.959 1 The extra coverage here appears legitimate. Validation ranges 1 and 2 really should have been combined. BX248353.1 249276 255947 1 0 1 BX248353.1 305695 323838 1 0.86 1 The extra coverage appears to be wrong BX248353.1 400793 409559 0.81 0 2 The two overlapping islands should have been merged. BX248353.1 727618 742674 1 0.037 1 BX248353.1 776521 795300 1 0.078 1 BX248353.1 1680222 1700449 1 0.08 1 BX248353.1 1866723 1880855 1 0.088 1 BX248353.1 2059672 2070753 1 0.226 1 The extra coverage appears to be legitimate BX248353.1 2115840 2144615 0.964 0.318 2 The extra coverage appears to be legitimate. Also splitting into two islands appears to be correct. BX248353.1 2213799 2242600 1 0.171 1 The extra coverage appears to be legitimate BX248353.1 2297077 2322967 1 0 1 Species Cronobacter sakazakii ATCC BAA-894 Comparison species in tree Genbank assemblies used GCF_000017665.1 GCF_000027065.2 GCF_001277235.1 GCF_001277195.1 GCF_000215745.1 Tree ((((C_sakazakii, C_turicensis)i0,C_dublinensis)i1,C_muytjensii)i2,E_aerogenes)i3; Start End Basewise coverage by xenoGI islands Extra Coverage Num overlapping xenoGI islands Notes CP000783.1 125239 132690 1 0 1 CP000783.1 263518 287078 1 0.063 1 CP000783.1 571545 601816 1 0.072 1 The extra coverage appears to be wrong. Families were assigned the wrong mrca here. CP000783.1 969835 1015482 0.692 0.301 2 This range has genes with a variety of mrcas. Thus xenoGI was correct to break it up into multiple islands. CP000783.1 1150997 1161514 0.725 0 2 It appears the two islands identified should have been merged. CP000783.1 1561010 1587672 0.391 0.084 3 This range has genes with a variety of mrcas. Thus xenoGI was correct to break it up into multiple islands. CP000783.1 1720214 1743995 0.949 0 1 CP000783.1 1907755 1914319 1 0 1 CP000783.1 1964491 1977651 0.771 0.271 3 The extra coverage and multiple islands appear to be correct CP000783.1 2237406 2272660 1 0.015 1 CP000783.1 2693304 2701447 1 0 1 CP000783.1 2974743 3022134 1 0.472 1 The extra coverage appears to be legitimate CP000783.1 3838625 3857813 0.672 0 5 It appears some of these islands should have been merged. The problem reflects some genes being assigned the wrong mrca CP000783.1 4214291 4221826 1 3.05 1 The extra coverage appears to be legitimate Species Streptococcus equi 4047 Comparison species in tree Genbank assemblies used GCF_000026585.1 GCF_000026605.1 GCF_000006785.2 GCF_000785515.1 GCF_000007465.2 Tree ((((S_equi,S_zooepidemicus)i0,S_pyogenes)i1,S_salivarius)i2,S_mutans)i3; Chromosome Start End Basewise coverage by xenoGI islands Extra Coverage Num overlapping xenoGI islands Notes FM204883.1 142548 182216 1 0 1 FM204883.1 746734 757321 0.564 0 1 FM204883.1 783708 825190 0.844 0 2 This range has genes with a variety of mrcas. Thus xenoGI was correct to break it up into multiple islands. FM204883.1 1206307 1271960 1 0.021 1 FM204883.1 1742042 1772823 1 0 1 FM204883.1 1991964 2006717 1 0 1 FM204883.1 2065120 2105533 0.982 0.183 1 The extra coverage appears to be legitimate Species Vibrio cholerae O1 biovar eltor str. N16961 Comparison species in tree Genbank assemblies used GCF_000006745.1 GCF_001558475.1 GCF_000011805.1 GCF_000196255.1 GCF_000146165.2 Tree ((((V_cholerae, V_mimicus)i0,V_fischeri)i1,P_profundum)i2,S_oneidensis)i3; Chromosome Start End Basewise coverage by xenoGI islands Extra Coverage Num overlapping xenoGI islands Notes AE003852.1 175343 189380 0.935 1.039 4 This range has genes with a variety of mrcas. Thus xenoGI was correct to break it up into multiple islands. The extra coverage appears to be legitimate. AE003852.1 520634 550262 0.915 0.068 1 AE003852.1 873242 915211 0.898 0.241 1 The extra coverage appears to be legitimate AE003852.1 1550108 1574355 1 0.697 1 This is the classic cholera toxin island. The genes in it are specific to V. cholerae, and not found in V. mimicus. It turns out a number of genes to either side are also V. cholerae specific, and xenoGI includes these in the island. Given the tree we have used, it appears to have done the right thing. AE003852.1 1895692 1952861 1 0.411 1 Some of the extra coverage here appears to be wrong. (The part to the left of the validaiton range) AE003853.1 308586 436632 0.991 0.025 1