An improved genome release (version Mt4.0) for the model legume Medicago truncatula

BMC Genomics

Table 1 Summary of sequencing libraries as input to the ALLPATHS-LG assembler

Type	Library name	Library size	# of reads	Sequence coverage (X-fold)	# of pairs	Pair coverage (X)
Frag	Illumina PE-200	207 ± 40	212,635,636	49.5	84,508,836	57.9
Frag	Illumina PE-376	244 ± 75	269,583,440	48.3	87,087,424	73.1
Frag	total		482,219,076	97.8	171,596,260	131.1
Jump	Illumina 3Kb	2014 ± 785	117,669,776	13.2	19,112,272	34
Jump	Illumina 4.5Kb	4866 ± 549	78,918,228	7.3	6,426,863	104.2
Jump	Illumina 5Kb	5062 ± 776	200,273,082	32.5	9,097,003	154.9
Jump	Illumina 7Kb	7455 ± 998	50,076,448	0.8	424,740	10.8
Jump	454 FLX 3Kb	2260 ± 816	1,499,510	0.4	440,037	3.7
Jump	total		448,437,044	54.2	35,500,915	307.7
Long_jump	Fosmid lib	35000 ± 7000	68,372	0	7,626	0.8
Long_jump	BAC lib mtrs	65000 ± 13000	40,080	0	9,269	1.9
Long_jump	BAC libs mte1 and mth2	100000 ± 20000	151,538	0	38,306	14.5
Long_jump	BAC lib mth4	200000 ± 40000	17,042	0	4,303	2.7
Long_jump	Total		277,032	0.1	59,504	19.9

Type refers to the ALLPATHS terminology of sequencing libraries - “frag” refers to short insert paired-end libraries that are typically two ends of <1Kb fragments, “jump” refers to long insert mate pair libraries that are typically between 1Kb to 10Kb, “long_jump” refers to the ends of fosmids and BACs.

ISSN: 1471-2164