Table 1.

Analysis of rearrangements in the mammalian mitochondrial genome reported in the NCBI database

	Taxonomic group	No. species	Genes differing in arrangement	Number confirmed	Number refuted	Endpoint errors noted	Present but not annotated	Genes or CR not present
	Monotremes	3	0	0	0	1	0	0
Marsupial	Didelphimorphia	4	16	16	0	0	1	4
	Paucituberculata	2	8	8	0	0	0	0
	Microbiotheria	1	4	4	0	0	0	3
	Diprotodontia	12	48	47	1	0	0	1
	Dasyuromorphia	6	32	24	8	0	0	0
	Notoryctemorphia	1	4	4	0	0	0	1
	Peramelemorphia	4	16	16	0	0	0	8
Eutheria	Afrosoricida	3	0	0	0	0	0	0
	Macroscelidea	2	0	0	0	0	0	0
	Tubulidentata	1	0	0	0	0	0	0
	Proboscidea	5	2	0	2	0	0	0
	Hyracoidea	2	1	0	1	0	0	0
	Sirenia	2	0	0	0	0	0	0
	Cingulata	1	0	0	0	0	0	0
	Pilosa	3	0	0	0	0	0	0
	Dermoptera	1	0	0	0	0	0	0
	Scandentia	1	0	0	0	0	0	0
	Primates	44	12	0	12	4	0	0
	Lagomorpha	6	0	0	0	0	0	0
	Rodentia	26	3	0	3	0	2	0
	Soricomorpha	5	2	0	2	0	0	0
	Erinaceomorpha	4	0	0	0	0	0	4
	Carnivora	65	9	0	9	3	0	1
	Pholidota	2	1	0	1	0	0	0
	Perissodactyla	9	0	0	0	0	0	0
	Artiodactyla	47	17	0	17	0	0	0
	Cetacea	32	12	0	12	1	0	0
	Chiroptera	10	0	0	0	0	0	0
	Total	304	187	119	68	9	3	22

Number of genes in mammalian mitochondrial genomes differing in position from that of humans (inferred to be the ancestral arrangement for all mammals) as reported in GenBank that were confirmed or refuted in this study, along with a summary of additional errors noted. See Additional file 1: Table S1 and Additional file 2: Table S2 for details. Each of the gene arrangement errors found brings into conformity a single shared gene arrangement for all of the marsupials and another shared gene arrangement that is shared among all monotremes and eutherians. On some mitogenomes, more than one annotation error was detected