Table 3. Statistics describing the distribution of different properties of RAD sequences after each step of filtering (FASTX-Toolkit), alignment to the eel draft genome (Bowtie) and assemblage into loci (Ref_map.pl).

FASTX
Species	Raw reads	Filtered reads	% Eliminated	Mean Q	Q1	Med	Q3	%A	%C	%G	%T
All	8 810 898	7 281 642	17.32	38.45	37.80	39.24	40	29.8	20.5	20.1	29.6
AA	8 769 831	7 007 835	19.92	38.36	37.72	39.10	40	29.7	20.5	20.1	29.6
AR	8 851 964	7 555 450	14.72	38.53	37.88	39.37	40	29.8	20.5	20.1	29.6

Bowtie
Species	Reads	Aligned	% Aligned	Nonaligned	% Nonaligned	Discarded	% Discarded
All	7 281 642	4 707 002	64.25	2 504 043	34.15	117 695	1.60
AA	7 007 835	4 768 089	67.16	2 218 176	31.22	115 152	1.63
AR	7 555 450	4 645 915	61.33	2 789 910	37.09	120 238	1.58

Ref_map
Species	Reads	Stacks	Loci	Loci used	% Loci used	Loci discarded	% Loci discarded
All	4 707 002	663 555	322 314	214 178	66.45	108 136	33.55
AA	4 768 089	745 193	333 871	224 896	67.36	109 309	32.74
AR	4 645 915	581 918	310 756	203 638	65.53	107 118	34.47

Abbreviations: AA, Anguilla anguilla; AR, A. rostrata; RAD, Restriction site Associated DNA.