Table 2.

Overview of nuclear variants retained with a coverage of ≥10 when mapping to the whale shark genome used for bait design (accession no. GCA_001642345.2)

Variant no.	Contig	Cov	Position of variant	Nucl. change	Mut type	Exon	Intron	Within probe range (±80 bp)	MAF	Gene
1	NW_018027618.1	10	81,300	T → A	TV		+	+	0.10
2	NW_018028177.1	10	361,879	G → A	TI	+		+	0.10	arhgap31
3	NW_018028334.1	10	259,900	C → T	TI		+	+	0.10
4	NW_018028334.1	10	259,937	A → G	TI		+	+	0.10
5	NW_018028334.1	10	259,952	C → T	TI		+	+	0.10
6	NW_018030239.1	10	300,687	A → G	TI		+	+	0.10
7	NW_018030239.1	10	300,695	A → T	TI		+	+	0.10
8	NW_018031751.1	10	272,654	AGTTTCTGT → AGT	DEL		+	+	0.30
9	NW_018031751.1	10	272,838	G → T	TV		+	+	0.10
10	NW_018032444.1	10	219,962	T → C	TI		+	+	0.10
11	NW_018033032.1	10	57,538	C → T	TI		+	+	0.10
12	NW_018034852.1	10	57,766	A → G	TI			–	0.10
13	NW_018035951.1	10	70,329	C → T	TI		+	+	0.10
14	NW_018048269.1	10	39,955	A → G	TI		+	+	0.10
15	NW_018049874.1	64	2,967	A → G	TI			–	0.05‬
16	NW_018055946.1	26	795,896	T → C	TI		+	–	0.23
17	NW_018055946.1	28	795,897	A → G	TI		+	–	0.21
18	NW_018056210.1	10	348,679	A → G	TI		+	+	0.10
19	NW_018061029.1	10	213,227	A → G	TI		+	+	0.10
20	NW_018067024.1	10	123,091	C → G	TV		+	+	0.10
21	NW_018071985.1	10	326,258	T → A	TV		+	+	0.10
22	NW_018071985.1	10	326,259	G → C	TV		+	+	0.10

Mut type: type of mutation, either transition (TI), transversion (TV) or deletion (DEL). Exon: variant occurs in exonic region (+). Intron: variant occurs in intronic region (+).

Abbreviations: Cov, coverage; MAF, minor allele frequency.