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Detailed information for vg0404388307:

Variant ID: vg0404388307 (JBrowse)	Variation Type: SNP
Chromosome: chr04	Position: 4388307
Reference Allele: G	Alternative Allele: A
Primary Allele: A	Secondary Allele: G

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.93, G: 0.07, others allele: 0.00, population size: 84. )

Flanking Sequence (100 bp) in Reference Genome:

TTTATCTAGAGTCCTAGTACTAGAGCACTTAGTATGAATACTAAATAATGAACCCGCAAAAATGGAAATATATTTTACTTAAACAAAGTAATTAAATAAC[G/A]
TAAGAAAGGAACACGAATGCTTACTTTATAGAAGAAGTTCTCCAAACCCGGAGCAGAGTGTACCGACAGCTCCGGTACTCCTCCAGAATTCCTCCTATGA

Reverse complement sequence

TCATAGGAGGAATTCTGGAGGAGTACCGGAGCTGTCGGTACACTCTGCTCCGGGTTTGGAGAACTTCTTCTATAAAGTAAGCATTCGTGTTCCTTTCTTA[C/T]
GTTATTTAATTACTTTGTTTAAGTAAAATATATTTCCATTTTTGCGGGTTCATTATTTAGTATTCATACTAAGTGCTCTAGTACTAGGACTCTAGATAAA

Allele Frequencies:

Populations	Population Size	Frequency of A(primary allele)	Frequency of G(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	40.40%	28.60%	6.52%	24.44%	NA
All Indica	2759	59.30%	20.50%	9.06%	11.13%	NA
All Japonica	1512	4.70%	49.40%	0.86%	45.04%	NA
Aus	269	39.40%	7.10%	11.52%	42.01%	NA
Indica I	595	93.80%	1.30%	0.67%	4.20%	NA
Indica II	465	64.10%	20.40%	8.17%	7.31%	NA
Indica III	913	37.70%	33.50%	14.35%	14.46%	NA
Indica Intermediate	786	55.60%	19.80%	9.80%	14.76%	NA
Temperate Japonica	767	1.30%	86.80%	0.26%	11.60%	NA
Tropical Japonica	504	8.70%	6.30%	1.59%	83.33%	NA
Japonica Intermediate	241	7.10%	20.30%	1.24%	71.37%	NA
VI/Aromatic	96	51.00%	3.10%	8.33%	37.50%	NA
Intermediate	90	52.20%	21.10%	6.67%	20.00%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0404388307	G -> DEL	N	N	silent_mutation	Average:24.536; most accessible tissue: Callus, score: 53.012	N	N	N	N
vg0404388307	G -> A	LOC_Os04g08230.1	downstream_gene_variant ; 2101.0bp to feature; MODIFIER	silent_mutation	Average:24.536; most accessible tissue: Callus, score: 53.012	N	N	N	N
vg0404388307	G -> A	LOC_Os04g08210-LOC_Os04g08230	intergenic_region ; MODIFIER	silent_mutation	Average:24.536; most accessible tissue: Callus, score: 53.012	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0404388307	NA	9.17E-11	mr1037	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
vg0404388307	NA	1.27E-06	mr1037_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
vg0404388307	NA	3.44E-11	mr1798_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