Mapping of Micro-Tom BAC-End Sequences to the Reference Tomato Genome Reveals Possible Genome Rearrangements and Polymorphisms

Table 1

Coverage of chromosomes by hypothetical Micro-Tom BAC contigs.

		SL2.40ch01	SL2.40ch02	SL2.40ch03	SL2.40ch04	SL2.40ch05	SL2.40ch06	SL2.40ch07	SL2.40ch08	SL2.40ch09	SL2.40ch10	SL2.40ch11	SL2.40ch12	Total (ch01–ch12)
Euchromatin	Chromosome length	27,903,720	24,734,122	16,423,960	13,871,288	10,836,573	17,576,248	17,480,118	15,552,430	10,522,300	9,129,273	11,175,203	12,034,427	187,239,662
Euchromatin	no. of Contigs	100	78	45	34	32	52	53	55	37	25	45	44	600
Euchromatin	no. of BACs	533	504	401	231	170	339	224	279	176	197	184	317	3,555
Euchromatin	Covered bases	17,310,734	14,644,412	11,678,941	6,261,540	5,377,576	10,621,719	8,336,310	9,541,847	6,047,365	5,473,701	6,855,876	8,119,058	110,269,079
Euchromatin	Uncovered bases	10,592,986	10,089,710	4,745,019	7,609,748	5,458,997	6,954,529	9,143,808	6,010,583	4,474,935	3,655,572	4,319,327	3,915,369	76,970,583
Euchromatin	% Coverage	62.0%	59.2%	71.1%	45.1%	49.6%	60.4%	47.7%	61.4%	57.5%	60.0%	61.3%	67.5%	58.9%
Heterochromatin	Chromosome length	62,400,524	25,184,172	48,416,754	50,193,024	54,184,865	28,465,388	47,788,503	47,480,227	57,139,791	55,705,032	42,210,822	53,451,826	572,620,928
Heterochromatin	no. of Contigs	175	74	147	131	169	76	135	150	149	159	128	155	1,648
Heterochromatin	no. of BACs	1,000	391	903	1,022	752	544	959	856	1,209	1,056	746	992	10,430
Heterochromatin	Covered bases	39,941,033	15,405,507	32,458,031	34,993,238	31,099,727	19,672,865	35,988,229	33,980,702	40,376,427	37,964,128	27,534,109	36,150,348	385,564,344
Heterochromatin	Uncovered bases	22,459,491	9,778,665	15,958,723	15,199,786	23,085,138	8,792,523	11,800,274	13,499,525	16,763,364	17,740,904	14,676,713	17,301,478	187,056,584
Heterochromatin	% Coverage	64.0%	61.2%	67.0%	69.7%	57.4%	69.1%	75.3%	71.6%	70.7%	68.2%	65.2%	67.6%	67.3%
Total	Chromosome length	90,304,244	49,918,294	64,840,714	64,064,312	65,021,438	46,041,636	65,268,621	63,032,657	67,662,091	64,834,305	53,386,025	65,486,253	759,860,590
Total	no. of Contigs	275	152	192	165	201	128	188	205	186	184	173	199	2,248
Total	no. of BACs	1,533	895	1,304	1,253	922	883	1,183	1,135	1,385	1,253	930	1,309	13,985
Total	Covered bases	57,251,767	30,049,919	44,136,972	41,254,778	36,477,303	30,294,584	44,324,539	43,522,549	46,423,792	43,437,829	34,389,985	44,269,406	495,833,423
Total	Uncovered bases	33,052,477	19,868,375	20,703,742	22,809,534	28,544,135	15,747,052	20,944,082	19,510,108	21,238,299	21,396,476	18,996,040	21,216,847	264,027,167
Total	% Coverage	63.4%	60.2%	68.1%	64.4%	56.1%	65.8%	67.9%	69.1%	68.6%	67.0%	64.4%	67.6%	65.3%