RNA sequencing read depth requirement for optimal transcriptome coverage in Hevea brasiliensis

BMC Research Notes

Table 5 Statistics of 1, 3 and 5 Gb assemblies of latex and leaf reads

k-mer size	Latex 1 Gb		Latex 3 Gb		Latex 5 Gb		Leaf 1 Gb		Leaf 3 Gb		Leaf 5 Gb
k-mer size	N50 (bp)	Total transcripts	N50 (bp)	Total transcripts	N50 (bp)	Total transcripts	N50 (bp)	Total transcripts	N50 (bp)	Total transcripts	N50 (bp)	Total transcripts
51	706	64,691	1016	89,882	1053	108,246	544	90,842	831	141,047	845	170,274
53	716	61,113	1058	85,854	1135	104,493	535	84,656	888	129,418	920	158,195
55	*724*	56,456	1093	79,303	1187	95,718	523	77,815	915	117,125	999	141,823
57	717	52,339	1102	73,610	1231	88,114	517	70,653	933	105,513	1049	127,329
59	707	48,151	*1108*	67,662	1266	80,620	509	64,286	*937*	95,662	1079	113,686
61	683	43,857	1100	62,627	*1281*	73,298	500	58,367	933	86,244	*1086*	100,912
63	668	40,003	1090	57,318	1270	67,227	490	52,086	912	78,666	1084	90,894
65	657	36,366	1067	53,173	1266	61,105	478	46,805	885	72,173	1059	82,529
67	642	32,702	1041	49,168	1241	55,834	466	41,495	855	66,289	1026	75,410
69	629	29,326	1001	46,360	1201	52,592	451	36,757	810	61,116	988	68,544
71	610	26,079	956	43,095	1151	49,302	439	32,167	761	56,152	944	63,072
73	591	23,055	907	40,051	1103	45,844	432	27,547	713	51,241	879	58,710
75	578	20,055	850	36,849	1052	42,945	427	23,246	669	46,727	823	53,571
77	567	17,326	815	33,398	990	39,996	427	19,079	631	41,838	763	49,712

The optimized N50 length for each tissue assembly is highlighted in bold italics.

ISSN: 1756-0500