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

BMC Research Notes

Table 3 Statistics of incremental bark assemblies across k-mers

k-mer size	1 Gb		3 Gb		5 Gb		8 Gb		10 Gb		13 Gb		16 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	N50 (bp)	Total transcripts
51	1,389	68,942	1,734	102,352	1,741	131,979	1,695	170,838	1,648	193,885	1,599	224,292	1,542	254,026
53	1,375	64,265	1,763	94,288	1,797	120,998	1,778	157,127	1,741	178,204	1,701	206,355	1,654	234,717
55	1,353	59,325	1,783	86,117	1,832	110,086	1,834	142,292	1,813	161,486	1,798	186,542	1,758	212,283
57	1,343	54,670	1,798	78,651	1,852	100,131	1,872	129,469	1,864	146,550	1,861	169,917	1,828	192,775
59	1,315	50,440	1,799	72,051	1,876	91,351	1,905	117,384	1,901	133,175	1,903	154,642	1,880	176,018
61	1,288	46,261	*1,804*	65,903	1,891	83,027	1,926	106,569	1,933	120,901	1,940	139,498	1,928	159,832
63	1,255	42,626	1,791	60,666	1,889	75,893	1,959	96,676	1,959	109,522	1,969	126,478	1,956	143,857
65	1,225	39,223	1,782	55,645	*1,900*	69,159	1,966	87,780	1,980	98,782	1,989	115,028	1,988	130,546
67	1,199	35,773	1,753	51,333	1,892	63,469	1,970	80,153	1,997	90,055	2,010	104,399	2,025	118,385
69	1,147	32,606	1,731	47,383	1,895	58,112	*1,976*	72,612	2,007	81,560	2,024	94,500	2,043	106,974
71	1,111	29,621	1,691	43,910	1,878	53,357	1,974	66,249	*2,017*	74,220	2,036	85,874	2,061	96,653
73	1,068	26,674	1,652	40,633	1,846	49,412	1,967	60,561	2,010	67,593	2,040	77,667	*2,068*	87,612
75	1,034	23,699	1,606	37,433	1,808	45,312	1,946	55,384	1,997	61,680	*2,041*	70,331	2,066	79,038
77	982	20,746	1,550	34,531	1,770	41,621	1,923	50,636	1,967	56,233	2,022	63,767	2,057	71,504

The peak N50 length from each datasize assembly (other than for 1 Gb) is highlighted in bold italics.

ISSN: 1756-0500