Transcriptome profiling shows gene regulation patterns in a flavonoid pathway in response to exogenous phenylalanine in Boesenbergia rotunda cell culture

Table 1 Summary of reads assembly generated by SOAPdenovo from control and phenylalanine treated Boesenbergia rotunda callus

	Control	Phenylalanine treated
Total number of reads	24473594	23470648
Total nucleotides (nt)	3671039100	3520597200
GC%	49.31%	47.89%
Q20%	95.13%	96.06%
Step-wise assembly
Total number of contig	287451	273979
Average sequence size of contigs	199	191
N50 length of contig	236	221
Total number of scaffolds	149648	147381
Average sequence size of scaffolds	359	330
N50 length of scaffold	535	465
Total number of unigenes	78998	77541
Total nucleotides (nt) in unigenes	44279890	39284596
Average sequence size of unigenes	561	507
N50 length of unigenes	703	610
Combined control and phenylalanine treated unigenes
Total number of all unigenes	101043
Average sequence size of all unigenes	599
N50 length of all unigenes	804
Unigenes with orientation	54284
Unigenes without orientation	46759

N50 size of contigs, scaffolds or unigene was calculated by ordering all sequences then adding the lengths from longest to shortest until the summed length exceeded 50% of the total length of all sequences.

ISSN: 1471-2164