Table 1.

Prophage prevalence by H. pylori ancestry.

H. pylori population	Total number of genomes	Genomes with prophage (n)	Genomes with prophages (%)	Genomes with complete prophages (n)	Genomes with complete prophages (%)	Proportion of complete prophages (%)
hspSWEuropeEAfricaUSA	17	13	76.5	0	0.	0.
hspEurasia2	78	43	55.1	13	16.7	30.2
hspSWEurope	175	64	36.6	24	13.7	37.5
hspSWEuropeChile	43	15	34.9	3	7.	20.
hspAfrica1MiscAmerica	21	7	33.3	1	5.	14.
hspAfrica1NAmerica	57	18	31.6	6	11.	33.
hspAfrica1WAfrica	7	2	29.	0	0.	0.
hspEurasia1	173	50	28.9	21	12.1	42.0
hspSahul	15	4	26.7	2	13.	50.
hspSWEuropeMiscAmerica	111	25	22.5	5	5.	20.
HpAsia2	34	8	23.5	5	15.	63.
hspAfrica1SAfrica	38	8	21.1	5	13.	63.
hspNEurope	50	10	20.0	0	0.	0.
hspEAsia	166	30	18.1	11	6.6	36.7
hspIndigenousAmerica	22	1	4.6	0	0.	0.
HpAfrica2	4	0	0.	0	0.	0.
Total	1011	298	29.5	96	9.5	32.2

Incomplete (or remnant) prophages are the majority (71.5%; 213/298) in H. pylori genomes. Out of the 213 genomes containing remnant prophages, 202 have incomplete prophages, while 11 have both complete and incomplete prophages.