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Detailed information for vg0404591448:

Variant ID: vg0404591448 (JBrowse)	Variation Type: SNP
Chromosome: chr04	Position: 4591448
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.91, A: 0.09, others allele: 0.00, population size: 213. )

Flanking Sequence (100 bp) in Reference Genome:

GCTCGGAGATTCCAAATGGACATTGATAGATTCAAAGCTAGAATACCCAGTGACCTGTGTCGTGCACTGTCGAGACAGTTTTGTCGCTATTGGCTCCCTC[G/A]
GAGAGATCTCCATGTTTAGTGGTAATAACACTGATGGTGTGGCTCTTCTCACGGCGAGCCCGTCACTGTTGATGCCTCCACCGGCACATATCTGCCAACG

Reverse complement sequence

CGTTGGCAGATATGTGCCGGTGGAGGCATCAACAGTGACGGGCTCGCCGTGAGAAGAGCCACACCATCAGTGTTATTACCACTAAACATGGAGATCTCTC[C/T]
GAGGGAGCCAATAGCGACAAAACTGTCTCGACAGTGCACGACACAGGTCACTGGGTATTCTAGCTTTGAATCTATCAATGTCCATTTGGAATCTCCGAGC

Allele Frequencies:

Populations	Population Size	Frequency of G(primary allele)	Frequency of A(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	92.40%	7.50%	0.04%	0.00%	NA
All Indica	2759	98.60%	1.40%	0.00%	0.00%	NA
All Japonica	1512	87.40%	12.60%	0.00%	0.00%	NA
Aus	269	72.90%	27.10%	0.00%	0.00%	NA
Indica I	595	100.00%	0.00%	0.00%	0.00%	NA
Indica II	465	99.80%	0.20%	0.00%	0.00%	NA
Indica III	913	96.50%	3.50%	0.00%	0.00%	NA
Indica Intermediate	786	99.40%	0.60%	0.00%	0.00%	NA
Temperate Japonica	767	93.50%	6.50%	0.00%	0.00%	NA
Tropical Japonica	504	83.10%	16.90%	0.00%	0.00%	NA
Japonica Intermediate	241	76.80%	23.20%	0.00%	0.00%	NA
VI/Aromatic	96	49.00%	50.00%	1.04%	0.00%	NA
Intermediate	90	92.20%	6.70%	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
vg0404591448	G -> A	LOC_Os04g08500.1	missense_variant ; p.Gly48Arg; MODERATE	nonsynonymous_codon ; G48R	Average:45.634; most accessible tissue: Zhenshan97 young leaf, score: 80.848	unknown	unknown	TOLERATED	0.09

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0404591448	2.17E-10	NA	mr1757	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
vg0404591448	1.19E-07	NA	mr1757	Jap_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
vg0404591448	1.24E-06	1.23E-06	mr1197_2	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
vg0404591448	5.15E-07	NA	mr1549_2	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