Table 1.

Small indels. The first half of the table summarises the numbers and types of indels detected in each group. The second half of the table shows the proportion of samples within a cluster that share each group-specific coding-region indel.

DOI: http://dx.doi.org/10.7554/eLife.12613.016

1. Number of indels			ISC002	ISC003	ISC004	ISC005	ISC006	ISC007	ISC008	ISC009	ISC010
Total number ofindels found within each group			58	60	73	79	65	55	55	84	60
Number of group-specific Indels shared by part of the strains of that group			9	5	11	12	7	0	8	22	7
Number of group-specific Indels shared by all the strains of that group			6	1	3	3	0	0	0	0	2
Number of group-specific Indels within coding regions			0	1	2	3	4	0	1	3	1
2. Indels within coding region
Gene ID	Gene product	Position	Type
LdBPK_310030	Aquaglyceroporin	Ld31_0007774	2		0.04
LdBPK_310030	Aquaglyceroporin	Ld31_0007735	2			1
LdBPK_310030	Aquaglyceroporin	Ld31_0007662	1				0.04
LdBPK_310030	Aquaglyceroporin	Ld31_0008099	2				0.11
LdBPK_291860	Putative historie H2A	Ld29_0816454	-2							0.25
LdBPK_040410	Conserved hypothetical protein	Ld04_0155491	3							0.08
LdBPK_070540	Conserved hypothetical protein	Ld07_0230487	-3						0.12
LdBPK_190080	Conserved hypothetical protein	Ldl9_0015151	1			0.04
LdBPK_261790	Conserved hypothetical protein	Ld26_0651748	4				0.11
LdBPK_301000	Conserved hypothetical protein	Ld30_0311376	-1			0.02
LdBPK_310690	Conserved hypothetical protein	Ld31_0241951	-3				0.11
LdBPK_332580	Conserved hypothetical protein	Ld33_0995960	1		0.04
LdBPK_366590	Conserved hypothetical protein	Ld36_2473775	-3								0.25
LdBPK_110650	hypothetical, unknown function	Ldll_0245832	-3	0.56
LdBPK_292330	hypothetical, unknown function	Ld29_1008496	-3							0.08