Massive parallel sequencing of mRNA in identification of unannotated salinity stress-inducible transcripts in rice (Oryza sativa L.)

Table 1 Numbers of mapped reads

Sample	Total filtered reads	Unique						Multiple	%	Unmapped	%
		total	%	genome	%	bridged	%
shoot_0 h	35,026,580	27,570,633	78.7	25,691,385	73.3	1,879,248	5.4	3,918,724	11.2	3,528,570	10.1
root_0 h	26,993,353	20,765,422	76.9	19,422,807	72.0	1,342,615	5.0	1,712,639	6.3	4,506,648	16.7
shoot_1 h	32,535,506	25,523,252	78.4	23,824,180	73.2	1,699,072	5.2	3,555,750	10.9	3,448,393	10.6
root_1 h	32,952,067	26,672,186	80.9	24,783,243	75.2	1,888,943	5.7	1,967,331	6.0	4,301,387	13.1

RNAs were prepared from normal shoot (shoot_0 h), normal root (root_0 h), shoot with salinity stress (shoot_1 h), or root with salinity stress (root_1 h). Numbers of 36-bp reads and their percentages of the total number of filtered reads, obtained by the summing of four technical replicates (Total filtered reads), are shown, as are reads mapped to the rice genome (Unique-genome), reads mapped uniquely to a predicted exon-exon bridging sequence (Unique-bridged), the total number of reads mapped uniquely to the genome and to a predicted exon-exon bridging sequence (Unique-total), reads mapped to multiple loci of the rice genome (Multiple), and reads unable to be mapped to the rice genome (Unmapped).

ISSN: 1471-2164