Supplementary Table 20 Identification and distribution of molecular variation (SNPs and INDELs) among 8 pseudomolecules Ca1 to Ca8 and unanchored genome sequence as Ca0

Chromosome	Deletions relative to the reference	Insertions relative to the reference	SNPs relative to the reference	Average SNP density per kb	Total variant count	Synonymous SNPs in genes	Non-synonymous SNPs in genes	Total SNPs in genes	Average variant density per kb
Ca1	17,398	14,580	263,670	5.5	295,648	24,517	7,231	31,748	6.1
Ca2	12,787	10,882	187,104	5.1	210,773	18,969	4,791	23,760	5.8
Ca3	11,539	9,613	167,855	4.2	189,007	16,611	4,936	21,547	4.7
Ca4	26,855	23,295	372,427	7.6	422,577	42,391	7,890	50,281	8.6
Ca5	13,530	11,015	203,188	4.2	227,733	14,893	5,216	20,109	4.7
Ca6	18,825	15,979	258,728	4.4	293,532	24,703	6,611	31,314	4.9
Ca7	16,322	13,755	227,005	4.6	257,082	20,584	5,362	25,946	5.3
Ca8	5,390	45,74	59,487	3.6	69,451	9,836	2,182	12,045	4.2
Ca0	61,179	45,370	2,389,343	13.6	2,495,892	47,451	21,819	69,270	1.4
Total	183,825	149,063	4,128,807	7.9	4,461,695	219,982	66,038	286,020	8.5