Table 1.

Genomic polymorphism summary.

Polymorphism	Total	Isolate
		Acacia	A517	BO5.10	1.01.12	Grape	GLO1	Geranium	Katie tomato	Davis navel	Rose	Noble rot	UKR	1.01.06
SNPs	980,329	216,299	335,768	173,741	202,270	357,305	213,332	205,957	127,779	180,103	166,813	169,336	240,348	172,830
Indels	157,936	28,232	39,506	20,843	26,030	46,303	28,064	24,380	16,330	22,044	21,823	19,990	29,151	22,141
Insertions	87,489	15,039	20,751	10,820	13,724	25,137	14,990	12,568	8492	11,424	11,529	10,197	15,354	11,536
Deletions	70,447	13,193	18,755	10,023	12,306	21,166	13,074	11,812	7838	10,620	10,294	9793	13,797	10,605
Largest insertion	58	58	57	56	58	58	58	56	56	56	57	56	59	56
Largest deletion	74	74	74	72	73	74	73	72	72	73	72	73	72	73
Change every (bp)	36	170	110	213	182	103	172	180	288	205	220	219	154	213
Changes per kb	28	6	9	5	5	10	6	6	3	5	5	5	6	5
Missense/Silent	0.755	0.705	0.689	0.737	0.755	0.673	0.733	0.741	0.721	0.731	0.745	0.741	0.719	0.735
Missense	98,400	21,831	34,264	18,091	21,529	34,489	22,031	22,285	12,807	18,700	17,589	18,049	25,784	17,916
Nonsense	1255	180	264	126	222	290	157	188	85	155	130	143	216	150
Silent	130,295	30,950	49,709	24,562	28,535	51,215	30,066	30,096	17,766	25,577	23,596	24,355	35,839	24,393
Major effect changes	5963	1113	1412	717	1037	1613	982	877	494	772	848	683	1090	743
Sequence depth		92	55	46	85	141	78	52	59	52	78	33	13	56

The total number of genomic polymorphisms per polymorphism type detailed per individual genotype in comparison to the T4 reference genome. The total shows the unique occurrence summation across all genotypes. Largest insertion and deletion are in bp.