Genome assembly quality assessment. Blast alignments were performed at the JGI web site (http://genome.jgi-psf.org/pages/blast.jsf?db=Emihu1) to examine the Emihu1 assembly (A) Hole in the genome. “Gold standard” gene 1 was compared to the genome. There is full coverage of the gene in both ESTs and RNAseq reads, but when compared to the genome, there is a part which does not have coverage. (B) Genomic Duplication. In building the “gold standard” genes several mapped to two contigs consistently, scaffold_11 from 810,000-910,000 and scaffold_385. Alignment of the two sequences is shown, with the segment from scaffold_11 as the query sequence. Duplication of almost the entire segment can be seen.