De novo sequencing and analysis of root transcriptome using 454 pyrosequencing to discover putative genes associated with drought tolerance in Ammopiptanthus mongolicus

Table 2 Assembly results of 454 data using various programs with default or optimized parameter

Parameter	Cap3	Newbler	Newbler (optimized parameter)	MIRA
Number of contigs	16,114	5,886	15,173	20,744
Total bases of contigs (bp)	7,665,534	4,380,563	7,348,496	9,060,888
Number of Contig ≥ 1000 bp	1,028	1,286	1,135	1,138
Contig N50 (bp)	462	948	491	436
Mean contig length (bp)	475.71	744.23	484.31	436.80
Number of singlets	19,605	72,556	13,883	67,537
Total bases of singlets (bp)	4,587,902	18,194,876	2,609,778	16,693,077
Total number of reads used in the assembly	635,229	582,278	640,951	587,297
Total number of reads used in the assembly	94.68%	86.65%	95.38%	87.40%
Contigs with significant hits^a	8,414	3,696	5,238	11,003
Contigs with significant hits^a	52.22%	62.79%	34.52%	53.04%
Contigs with 80% or greater coverage^b	58	65	84	74
Contigs with 80% or greater coverage^b	0.3599%	1.104%	0.5536%	0.3567%
Soybean protein hits^c	5,332	2,596	3,657	5,528
Soybean protein hits^c	9.558%	4.653%	6.560%	9.909%
Soybean proteins with 80% or greater coverage^d	44	60	84	66
Soybean proteins with 80% or greater coverage^d	0.0079%	0.1076%	0.1506%	0.1183%

^a Contigs showing significant hits (E < 1e-5) with soybean proteins. ^b Contigs showing 80% or greater coverage of soybean proteins. ^c Unique soybean proteins to which contigs show significant hits (E < 1e-5). ^d Unique soybean proteins to which contigs show 80% or greater coverage.

ISSN: 1471-2164