Table 1

de novo assembly statistics
a.
Longest Contig 10111
Contig N50 740
Contig N90 172
Longest Scaffold 3641215
Scaffold N50 452028
Scaffold N90 56222
Number of Scaffolds 9714
b.
Root Leaf Stem Flower
Reads 4566554 4372192 5429138 5058312
kmers 57670643 55530204 67596347 60219435
Inchworm contigs 148819 148700 172507 150126
Total transcripts 27916 27369 34518 31223
c.
Features Average S.D.
Number of genes 20169 -
Gene length 1695.95 1526.01
Exon length 208.28 210.62
Intron length 388.62 393.41
Number of exons 3.5 2.96
Number of introns 2.5 2.96
Exonic GC% 42.74 5
Intronic GC% 30.04 7.09

The respective assembly statistics are summarized from various sequencing libraries using (a) SOAPdenovo [16] for the genome and (b) Trinity [35] for the transcriptomes. Various annotation statistics for genes, exons and introns are also provided (c).

Krishnan et al.

Krishnan et al. BMC Genomics 2012 13:464   doi:10.1186/1471-2164-13-464

Open Data