Table 1.

Transcriptome assembly (BinPacker CD-hit-est Transrate Corrected) performance metrics for: contig number, TransRate score (Score), BUSCO indices: % single copy orthologs (% SCO), % duplicated copy orthologs (% DCO), % fragmented (% frag), and % missing (% miss), as well as Salmon mapping rates (% mapping) for the optimized testes assembly. Dammit transcriptome assembly annotation statistics, including searches in the program TransDecoder for open reading frames (ORFs) and searches for homologous sequences in five databases: Rfam, Pfam-A, Uniref90, OrthoDB, and BUSCO. Percentages were calculated from the count number of each parameter divided by the total number of contigs in the transcriptome (155,134). The only exception to this calculation is for complete ORFs, which were calculated as a percentage of the total ORFs (75,482). The BUSCO results for the annotated assembly are not shown here as they are identical to those for the un-annotated assembly

Transcriptome Assembly Statistics
Contig #	Score	% SCO	% DCO	% frag	% miss	% mapping
155,134	0.335	77	27	5.9	16	92.14
Dammit Annotation Statistics
Search Type	TransDecoder		Rfam	Pfam-A	Uniref90	OrthoDB	Dammit
Parameter	Total ORFs	Complete ORFs	ncRNAs	Protein Domains	Proteins	Orthologs	Total Annotated Contigs
Count	75,482	43,028	937	25,675	62,865	51,806	77,915
Percentage	48.7%	57.0%	0.6%	16.6%	40.5%	33.4%	50.2%