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Detailed information for vg0411783837:

Variant ID: vg0411783837 (JBrowse)	Variation Type: SNP
Chromosome: chr04	Position: 11783837
Reference Allele: G	Alternative Allele: T
Primary Allele: G	Secondary Allele: T

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.01, others allele: 0.00, population size: 281. )

Flanking Sequence (100 bp) in Reference Genome:

GAATGTTGATGGAGAAGTTGTAATATTTTTGGACAAAATTCTTAGTGCTAGAAGTTGTTATATTTTAAGACAGAGGGATTATTGTTTAGAATATAGATCT[G/T]
GGTATATGAAAATAACATGGCCAAATTCGTTATATCAAAAAAGCTTTCATAATGTCACGCTTCTGCAACTCATTTTGGATTTATGGAATTGAATTAAGTG

Reverse complement sequence

CACTTAATTCAATTCCATAAATCCAAAATGAGTTGCAGAAGCGTGACATTATGAAAGCTTTTTTGATATAACGAATTTGGCCATGTTATTTTCATATACC[C/A]
AGATCTATATTCTAAACAATAATCCCTCTGTCTTAAAATATAACAACTTCTAGCACTAAGAATTTTGTCCAAAAATATTACAACTTCTCCATCAACATTC

Allele Frequencies:

Populations	Population Size	Frequency of G(primary allele)	Frequency of T(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	97.40%	2.10%	0.47%	0.00%	NA
All Indica	2759	95.70%	3.60%	0.80%	0.00%	NA
All Japonica	1512	99.90%	0.10%	0.00%	0.00%	NA
Aus	269	100.00%	0.00%	0.00%	0.00%	NA
Indica I	595	90.60%	8.10%	1.34%	0.00%	NA
Indica II	465	97.60%	2.20%	0.22%	0.00%	NA
Indica III	913	97.80%	2.20%	0.00%	0.00%	NA
Indica Intermediate	786	95.80%	2.50%	1.65%	0.00%	NA
Temperate Japonica	767	99.90%	0.10%	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	98.90%	1.10%	0.00%	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
vg0411783837	G -> T	LOC_Os04g20960.1	5_prime_UTR_premature_start_codon_gain_variant ; LOW	silent_mutation	Average:45.959; most accessible tissue: Minghui63 panicle, score: 62.157	N	N	N	N
vg0411783837	G -> T	LOC_Os04g20960.1	5_prime_UTR_variant ; 470.0bp to feature; MODIFIER	silent_mutation	Average:45.959; most accessible tissue: Minghui63 panicle, score: 62.157	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0411783837	4.57E-07	NA	mr1946	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
vg0411783837	1.91E-08	1.63E-07	mr1946	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