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Detailed information for vg1105412239:

Variant ID: vg1105412239 (JBrowse)	Variation Type: SNP
Chromosome: chr11	Position: 5412239
Reference Allele: G	Alternative Allele: T
Primary Allele: G	Secondary Allele: T

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.99, others allele: 0.00, population size: 268. )

Flanking Sequence (100 bp) in Reference Genome:

GCAATCTAAAATCAGATAGTACGTATCTTGCTGCTAAGAATCTGGCTTGATTCGTAATACTAGATTACGTCATATCCAATCCTATGTTGCTATATTATGG[G/T]
AAGTAGGGAGTACTTCTTTATAATTATATATGTACATTTTGGTCAGTCTAATTTCCGTTCCTTAGTACATACAATTAGTTCAAAATCGACTATTATGTTT

Reverse complement sequence

AAACATAATAGTCGATTTTGAACTAATTGTATGTACTAAGGAACGGAAATTAGACTGACCAAAATGTACATATATAATTATAAAGAAGTACTCCCTACTT[C/A]
CCATAATATAGCAACATAGGATTGGATATGACGTAATCTAGTATTACGAATCAAGCCAGATTCTTAGCAGCAAGATACGTACTATCTGATTTTAGATTGC

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	97.10%	2.80%	0.02%	0.00%	NA
All Indica	2759	100.00%	0.00%	0.00%	0.00%	NA
All Japonica	1512	91.50%	8.50%	0.07%	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	100.00%	0.00%	0.00%	0.00%	NA
Indica III	913	100.00%	0.00%	0.00%	0.00%	NA
Indica Intermediate	786	100.00%	0.00%	0.00%	0.00%	NA
Temperate Japonica	767	96.10%	3.90%	0.00%	0.00%	NA
Tropical Japonica	504	89.10%	10.90%	0.00%	0.00%	NA
Japonica Intermediate	241	81.70%	17.80%	0.41%	0.00%	NA
VI/Aromatic	96	93.80%	6.20%	0.00%	0.00%	NA
Intermediate	90	100.00%	0.00%	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
vg1105412239	G -> T	LOC_Os11g10060.1	downstream_gene_variant ; 4742.0bp to feature; MODIFIER	silent_mutation	Average:64.859; most accessible tissue: Callus, score: 88.546	N	N	N	N
vg1105412239	G -> T	LOC_Os11g10060-LOC_Os11g10070	intergenic_region ; MODIFIER	silent_mutation	Average:64.859; most accessible tissue: Callus, score: 88.546	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1105412239	3.89E-06	NA	mr1742_2	Jap_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