Table 3.

Total number and type of SNPs in the 20 Pt isolates.

Isolate	SNPs	Ref.homo	Data.missing	Intergenic	Intronic	p5UTR	p3UTR	Coding	SYN	NSY	Read-Through	Nonsense	Homozygous	Heterozygous	% Intergenic	% coding	coding versus intronic	% SYN	% NSY	% homozygous	% heterozygous	3UTR vs 5UTR
760285	398,470	105,557	189,074	332,036	12,804	3032	5566	45,032	16,756	27,346	177	753	50,091	348,379	83.3	11.3	3.52	37.2	60.7	12.6	87.4	1.84
630846	406,525	142,134	144,442	339,081	13,032	3046	5718	45,648	16,966	27,764	186	732	51,387	355,138	83.4	11.2	3.50	37.2	60.8	12.6	87.4	1.88
790197	408,240	143,658	141,203	340,482	13,090	3088	5692	45,888	17,034	27,927	179	748	51,164	357,076	83.4	11.2	3.51	37.1	60.9	12.5	87.5	1.84
670028	407,573	145,214	140,314	340,042	12,998	3094	5646	45,793	17,009	27,842	180	762	50,900	356,673	83.4	11.2	3.52	37.1	60.8	12.5	87.5	1.82
730003	407,980	142,704	142,417	340,387	13,005	3085	5650	45,853	17,026	27,876	180	771	51,068	356,912	83.4	11.2	3.53	37.1	60.8	12.5	87.5	1.83
66-L-3	406,826	141,290	144,985	339,294	13,070	3065	5658	45,739	17,000	27,801	176	762	51,046	355,780	83.4	11.2	3.50	37.2	60.8	12.5	87.5	1.85
60-L-2	329,330	138,842	224,929	275,507	10,245	2401	4521	36,656	13,457	22,426	161	612	71,613	257,717	83.7	11.1	3.58	36.7	61.2	21.7	78.3	1.88
64-L-3	341,857	231,639	119,605	286,364	10,622	2485	4680	37,706	13,820	23,087	159	640	93,995	247,862	83.8	11.0	3.55	36.7	61.2	27.5	72.5	1.88
630550	405,461	140,326	147,314	338,131	13,039	3105	5679	45,507	16,898	27,691	179	739	51,021	354,440	83.4	11.2	3.49	37.1	60.8	12.6	87.4	1.83
BCL 75	402,732	131,151	159,218	335,854	12,884	3051	5644	45,299	16,768	27,590	184	757	50,794	351,938	83.4	11.2	3.52	37.0	60.9	12.6	87.4	1.85
750299	409,340	145,799	137,962	341,488	13,118	3059	5709	45,966	17,021	27,990	181	774	51,282	358,058	83.4	11.2	3.50	37.0	60.9	12.5	87.5	1.87
700201	409,220	142,703	141,178	341,472	13,034	3109	5678	45,927	17,059	27,941	179	748	51,747	357,473	83.4	11.2	3.52	37.1	60.8	12.6	87.4	1.83
740408	410,194	150,429	132,478	342,294	13,113	3094	5678	46,015	17,030	28,060	181	744	51,371	358,823	83.4	11.2	3.51	37.0	61.0	12.5	87.5	1.84
740606	409,683	147,405	136,013	341,821	13,075	3086	5705	45,996	17,073	27,983	184	756	51,162	358,521	83.4	11.2	3.52	37.1	60.8	12.5	87.5	1.85
700575	404,032	125,345	163,724	336,920	12,925	3064	5632	45,491	16,911	27,631	178	771	50,727	353,305	83.4	11.3	3.52	37.2	60.7	12.6	87.4	1.84
QWRI	402,731	125,706	164,664	335,748	12,885	3068	5627	45,403	16,861	27,623	177	742	50,179	352,552	83.4	11.3	3.52	37.1	60.8	12.5	87.5	1.83
900084	435,758	95,663	161,680	364,218	13,846	3274	5929	48,491	18,119	29,320	197	855	82,591	353,167	83.6	11.1	3.50	37.4	60.5	19.0	81.0	1.81
900273	443,430	107,865	141,806	370,693	14,034	3288	6048	49,367	18,365	29,943	192	867	85,005	358,425	83.6	11.1	3.52	37.2	60.7	19.2	80.8	1.84
89-L-1	446,048	117,590	129,463	372,899	14,131	3328	6057	49,633	18,478	30,076	195	884	85,572	360,476	83.6	11.1	3.51	37.2	60.6	19.2	80.8	1.82
890155	408,368	133,523	151,210	340,839	13,002	3129	5610	45,788	17,002	27,825	182	779	51,566	356,802	83.5	11.2	3.52	37.1	60.8	12.6	87.4	1.79

Ref.homo, homozygous reference alleles for the genotype calling.

Data.missing, missing data at the SNP sites concatenated from all of the 20 isolates.

For each isolate, number of SNPs, Ref.homo, and Data.missing added up to 693,101 SNPs concatenated from all of the isolates.

UTR, untranslated region; SYN, Synonymous SNPs; NSY, Non-synonymous SNPs.

SNPs, total SNP identified in an isolate, which included intergenic, intronic, SNPs in UTRs and in coding regions;

SNPs in coding regions were further classified as SYN, NSY, read-through, and nonsense SNPs.

% Intergenic, Intergenic SNPs/total SNPs identified per isolate; % coding, Coding SNPs/total SNPs identified per isolate.

% NSY, percentage of Non-synonymous SNPs/Coding SNPs; % SYN, percentage of Synonymous SNPs/Coding SNPs.