Table 1:

Contamination screening of the H. bacteriophora assembly

Number of scaffolds	Sum of scaffold spans (bp)	Mean coveragea	Best matches in NCBI nt database	Assignment
12	99,556	2.8	Stenotrophomonas maltophilia genome	Bacterial culture contaminantb
4	4,709	0.1	Photorhabdussp. genomes	Symbiont culture contaminantb
2	2,144	756.0	Poorly annotated mitochondrial matches	H. bacteriophora mitochondrial fragments
22	3,051,844	69.6	Mariner transposons in Metazoa, especially Hymenoptera and Platyhelminthes	H. bacteriophora nuclear genome mariner transposon family (highest coverage 960-fold)
10	334,100	76.6	Low score match to several histone H3.3 across Metazoa	H. bacteriophora nuclear sequence
7	713,932	56.5	Chance nucleotide matches to conserved genes in other taxa	H. bacteriophora nuclear sequences

^aThe average read coverage of the whole assembly was 85.3.

^bThese scaffolds were removed by the low-coverage filter.