Molecular response to the pathogen Phytophthora sojae among ten soybean near isogenic lines revealed by comparative transcriptomics

Table 1 Statistics of pair-end reads in RNA sequencing experiment

Soybean line	Raw reads	Clean reads^a	Uniquely mapped reads^b	% of uniquely mapped reads^c
Inoculated Group
Williams (rps)	50,126,404	39,475,154	28,222,946	71.5
Union (Rps1-a)	25,614,448	20,169,804	14,969,954	74.2
L77-1863 (Rps1-b)	28,308,350	22,460,578	16,591,206	73.9
L75-3735 (Rps1-c)	19,696,090	15,483,052	11,084,896	71.6
Williams82 (Rps1-k)	14,508,392	13,527,604	11,527,676	85.2
L83-570 (Rps3-a)	21,982,116	17,531,234	12,954,567	73.9
L91-8347 (Rps3-b)	32,063,808	25,210,242	18,704,692	74.2
L92-7857 (Rps3-c)	29,003,280	22,775,218	16,776,075	73.7
L85-2352 (Rps4)	27,891,876	21,857,446	15,860,686	72.6
L85-3059 (Rps5)	35,204,260	30,651,204	24,816,154	81.0
L89-1581 (Rps6)	26,761,058	23,224,142	19,322,975	83.2
Mock-inoculated Group
Williams (rps)	21,949,578	20,385,960	17,841,238	87.5
Union (Rps1-a)	25,680,502	23,860,934	20,936,764	87.7
L77-1863 (Rps1-b)	20,303,214	18,830,218	16,453,627	87.4
L75-3735 (Rps1-c)	26,452,482	22,841,526	19,049,873	83.4
Williams82 (Rps1-k)	19,289,852	16,845,090	14,241,574	84.5
L83-570 (Rps3-a)	33,576,796	29,006,366	24,493,712	84.4
L91-8347 (Rps3-b)	25,609,764	23,775,078	20,880,124	87.8
L92-7857 (Rps3-c)	24,806,160	22,983,728	20,078,725	87.4
L85-2352 (Rps4)	24,677,426	22,899,582	20,085,744	87.7
L85-3059 (Rps5)	26,874,804	23,304,436	19,637,730	84.3
L89-1581 (Rps6)	27,363,314	25,362,532	22,151,262	87.3

^aReads with a quality score less than 20 and length less than 101 nucleotides were excluded.
^bReads uniquely mapped to G. max genome assembly (v1.0) using TopHat 2.0 software [58].
^cPercentage of uniquely mapped reads out of clean reads.

ISSN: 1471-2164