Table 4.

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

Type	Alphonso genome			Tommy Atkins genome
	Huania	Pahob	Carabaoc	Huania	Pahob	Carabaoc
3 prime UTR truncation					1
3 prime UTR variant	6,098	5,528	4,744	10,397	9,645	8,874
5 prime UTR truncation		3	3	2		3
5 prime UTR variant	3,913	3,489	2,987	6,417	5,935	5,265
Bidirectional gene fusion	3	1	1	5	2	4
Conservative inframe deletion	708	579	550	587	489	502
Conservative inframe insertion	796	746	643	664	637	564
Disruptive inframe deletion	1,266	1,086	1,026	1,114	947	907
Disruptive inframe insertion	842	706	682	743	692	669
Downstream gene variant	299,752	273,125	225,389	244,707	228,871	194,277
Exon loss variant		4	3	5	3	4
Frameshift variant	7,571	6,757	6,054	5,307	4,857	4,371
Intergenic region	422,962	380,721	318,804	369,574	338,484	296,065
Intragenic variant	2	4	4	21	21	17
Intron variant	83,767	75,690	65,064	123,064	114,750	102,061
Non-coding transcript variant	118	98	74	267	209	184
Splice acceptor variant	151	147	129	229	221	177
Splice donor variant	252	187	178	287	244	240
Splice region variant	2,412	2,078	1,851	2,815	2,647	2,375
Start lost	112	108	90	104	94	93
Start retained variant	11	9	7	9	8	12
Stop gained	242	212	188	198	192	170
Stop lost	96	80	88	75	76	70
Stop retained variant	11	13	8	11	12	13
Upstream gene variant	335,143	307,696	249,591	275,331	258,779	215,457

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