Deleterious SNPs – MyNutRiceBase

Search putative deleterious SNPs in genome sequences:

Traits:

Class:

RAPDB ID:

MSU ID:

R498 ID:

Gene descriptions:

SIFT score:

Allele:

Traits	Class	RAPDB ID	MSU ID	R498 ID	Gene symbol	Gene category	Gene descriptions	SNP ID	SIFT score	SIFT prediction	Ref allele	Allele	Chr	Pos	Ref AA	Allele AA	AA pos	Bali	PH9	MRM16	MRQ100	MR297	MRQ76	RAPDB transcript ID	SIFT median	Num. of seqs	dbSNP
salicylic acid	Biochemical	Os01g0358400	LOC_Os01g25610	OsR498G0100935300.01	RPS4	NA	40S ribosomal protein S4, putative, expressed	chr01_14514480	0.04	DELETERIOUS	A	G	chr01	14,514,480	I	V	92	AG	AA	AA	AA	AA	AA	OS01T0358400-01	2.65	201	novel
drought tolerance	Abiotic Stress	Os01g0358400	LOC_Os01g25610	OsR498G0100935300.01	RPS4	NA	40S ribosomal protein S4, putative, expressed	chr01_14514480	0.04	DELETERIOUS	A	G	chr01	14,514,480	I	V	92	AG	AA	AA	AA	AA	AA	OS01T0358400-01	2.65	201	novel
BLB	Biotic stress	Os01g0383900	LOC_Os01g28690	OsR498G0101004300.01	APIP12	NA	nucleoporin autopeptidase domain containing protein, expressed	chr01_16062855	0.04	DELETERIOUS	A	G	chr01	16,062,855	S	G	3	AG	AA	AG	AG	AG	AG	OS01T0383900-01	3.15	5	rs18634483
shoot	Morphology	Os01g0142800	LOC_Os01g04950	OsR498G0100152900.01	OsPTR7,PTR7	NA	peptide transporter PTR2, putative, expressed	chr01_2296920	0.00	DELETERIOUS	C	T	chr01	2,296,920	R	W	223	CT	CT	CT	CT	CT	CC	OS01T0142800-02	3.43	9	novel
grain	Agronomical	Os01g0142800	LOC_Os01g04950	OsR498G0100152900.01	OsPTR7,PTR7	NA	peptide transporter PTR2, putative, expressed	chr01_2296920	0.00	DELETERIOUS	C	T	chr01	2,296,920	R	W	223	CT	CT	CT	CT	CT	CC	OS01T0142800-02	3.43	9	novel
transporter	Biochemical	Os01g0142800	LOC_Os01g04950	OsR498G0100152900.01	OsPTR7,PTR7	NA	peptide transporter PTR2, putative, expressed	chr01_2296920	0.00	DELETERIOUS	C	T	chr01	2,296,920	R	W	223	CT	CT	CT	CT	CT	CC	OS01T0142800-02	3.43	9	novel
endosperm	Morphology	Os01g0601000	LOC_Os01g41720	OsR498G0101477000.01	OsEnS-10	NA	expressed protein	chr01_23611397	0.01	DELETERIOUS	A	G	chr01	23,611,397	S	P	461	AA	AG	AA	AA	AA	AA	OS01T0601000-00	3.41	20	novel
endosperm	Morphology	Os01g0601000	LOC_Os01g41720	OsR498G0101477000.01	OsEnS-10	NA	expressed protein	chr01_23611652	0.01	DELETERIOUS	T	G	chr01	23,611,652	Q	P	433	TG	TT	TG	TT	TT	TG	OS01T0601000-00	3.41	19	novel
culm	Morphology	Os01g0612700	LOC_Os01g42710	OsR498G0101532700.01	OsLOL5,OsLSD5,LOL5,LOL2,OsLOL2	LOL5	retrotransposon protein, putative, unclassified, expressed	chr01_24294974	0.01	DELETERIOUS	C	T	chr01	24,294,974	P	L	228	CT	CC	CT	CT	CT	CT	OS01T0612700-01	2.70	10	novel
lodging drawf	Abiotic Stress	Os01g0612700	LOC_Os01g42710	OsR498G0101532700.01	OsLOL5,OsLSD5,LOL5,LOL2,OsLOL2	LOL5	retrotransposon protein, putative, unclassified, expressed	chr01_24294974	0.01	DELETERIOUS	C	T	chr01	24,294,974	P	L	228	CT	CC	CT	CT	CT	CT	OS01T0612700-01	2.70	10	novel
Traits	Class	RAPDB ID	MSU ID	R498 ID			Gene descriptions		SIFT score			Allele