Table 3.

Functional annotation of the detected SNP variants in three Philippine mango species

Type	Alphonso genome			Tommy Atkins genome
	Huania	Pahob	Carabaoc	Huania	Pahob	Carabaoc
3 prime UTR variant	34,712	26,993	21,424	58,036	46,735	36,749
5 prime UTR premature start codon gain variant	3,076	2,351	1,821	4,850	3,751	2,897
5 prime UTR variant	19,305	14,370	11,386	30,836	24,082	18,839
Downstream gene variant	1,903,377	1,501,470	1,139,595	1,570,171	1,300,734	968,689
Initiator codon variant	30	24	18	32	33	25
Intergenic region	3,033,446	2,310,351	1,862,224	2,801,150	2,196,966	1,811,990
Intragenic variant				104	80	35
Intron variant	528,400	412,723	327,832	823,307	675,164	538,294
Missense variant	125,037	91,959	79,309	111,102	88,532	73,636
Splice acceptor variant	643	494	411	731	580	491
Splice donor variant	545	406	345	711	584	486
Splice region variant	16,351	12,542	10,269	18,521	14,905	12,266
Start lost	302	214	207	183	147	113
Start retained variant	13	9	8
Stop gained	2,601	1,887	1,651	1,630	1,393	1,055
Stop lost	492	339	304	309	231	190
Stop retained variant	191	154	140	143	133	102
Synonymous variant	87,448	63,950	54,816	86,133	66,813	55,417
Upstream gene variant	2,040,834	1,627,526	1,203,524	1,702,492	1,419,809	1,026,224

^aM. odorata, ^bM. altissima, ^cM. indica