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Detailed information for vg0204550038:

Variant ID: vg0204550038 (JBrowse)	Variation Type: SNP
Chromosome: chr02	Position: 4550038
Reference Allele: G	Alternative Allele: T,C
Primary Allele: G	Secondary Allele: C

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.99, others allele: 0.00, population size: 245. )

Flanking Sequence (100 bp) in Reference Genome:

GCTATCCTAGTACGAATAGTATTCATGGTATCATCATTCTCTGCATCTTCACTCTCATCGTCTGACGTGTCACTTGTATCTTCTATTAAGTAGTCCTCAT[G/T,C]
AGCATCACATCTCTCAAACTCCTTATCACGTAAATTGCTATCACGGACGAAGTTATGCATAGCAAGACAAGCCATGATGATATGCTTCTGAGTAGTAGGT

Reverse complement sequence

ACCTACTACTCAGAAGCATATCATCATGGCTTGTCTTGCTATGCATAACTTCGTCCGTGATAGCAATTTACGTGATAAGGAGTTTGAGAGATGTGATGCT[C/A,G]
ATGAGGACTACTTAATAGAAGATACAAGTGACACGTCAGACGATGAGAGTGAAGATGCAGAGAATGATGATACCATGAATACTATTCGTACTAGGATAGC

Allele Frequencies:

Populations	Population Size	Frequency of G(primary allele)	Frequency of C(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	99.80%	0.10%	0.02%	0.00%	T: 0.02%
All Indica	2759	99.80%	0.20%	0.00%	0.00%	T: 0.04%
All Japonica	1512	100.00%	0.00%	0.00%	0.00%	NA
Aus	269	100.00%	0.00%	0.00%	0.00%	NA
Indica I	595	100.00%	0.00%	0.00%	0.00%	NA
Indica II	465	99.40%	0.60%	0.00%	0.00%	NA
Indica III	913	100.00%	0.00%	0.00%	0.00%	NA
Indica Intermediate	786	99.60%	0.30%	0.00%	0.00%	T: 0.13%
Temperate Japonica	767	100.00%	0.00%	0.00%	0.00%	NA
Tropical Japonica	504	100.00%	0.00%	0.00%	0.00%	NA
Japonica Intermediate	241	100.00%	0.00%	0.00%	0.00%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	97.80%	1.10%	1.11%	0.00%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0204550038	G -> T	LOC_Os02g08450.1	missense_variant ; p.His613Asn; MODERATE	N	Average:24.768; most accessible tissue: Minghui63 panicle, score: 42.799	N	N	N	N
vg0204550038	G -> C	LOC_Os02g08450.1	missense_variant ; p.His613Asp; MODERATE	N	Average:24.768; most accessible tissue: Minghui63 panicle, score: 42.799	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0204550038	8.13E-06	7.06E-06	mr1004_2	Ind_All	Not	Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0204550038	4.37E-07	4.55E-07	mr1172_2	Ind_All	YES	Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251