Table 1.

Total Illumina reads for each of the Musca domestica strains/lines tested

Sample	SRA* accession	Total PE** reads passing chastity filter	Discarded‡	Reads used
aabys	SRR521286	40284931	2794419	37490512
CS	SRR521290	34589399	2561540	32027859
ALHF	SRR521289	30329576	2208815	28120761
ALHF- replicate	SRR521288	26151304	1406309	24744995

^*Sequence Read Archive, National Center for Biotechnology Information (http://www.ncbi.nlm.nih.gov/sra/).

^**51 nt Paired-end reads with an average insert size of 200 nt.

^‡Discarded reads were removed using Trimmomatic based on a sliding window quality cut off of (4:15) and a minimum length of 36 nt after adapter removal. In addition all mate pairs were excluded from analysis if one of the mate pairs was rejected by Trimmomatic.