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Detailed information for vg1000744795:

Variant ID: vg1000744795 (JBrowse)	Variation Type: SNP
Chromosome: chr10	Position: 744795
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.99, A: 0.01, others allele: 0.00, population size: 113. )

Flanking Sequence (100 bp) in Reference Genome:

TAACTAAAAATCAAGAGATAGATATTAATGCTATGTGATAGTTTGAGAGCGATTTTAGATTGCTACGTGGCGGTTTAGGAGCGTTTATAGCAAGTTTAAT[G/A]
GACTTTTAGTATATAATAGATAGATAAATAAATAGATATGGATAATGCTAAAAAGTCTTATAACAGTAGCAGCAGTAGTCTAGGTGCACTTCATTTAGGC

Reverse complement sequence

GCCTAAATGAAGTGCACCTAGACTACTGCTGCTACTGTTATAAGACTTTTTAGCATTATCCATATCTATTTATTTATCTATCTATTATATACTAAAAGTC[C/T]
ATTAAACTTGCTATAAACGCTCCTAAACCGCCACGTAGCAATCTAAAATCGCTCTCAAACTATCACATAGCATTAATATCTATCTCTTGATTTTTAGTTA

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	64.60%	21.90%	3.15%	10.35%	NA
All Indica	2759	59.60%	31.00%	2.94%	6.42%	NA
All Japonica	1512	72.90%	2.70%	4.17%	20.17%	NA
Aus	269	55.00%	45.00%	0.00%	0.00%	NA
Indica I	595	40.30%	52.80%	4.03%	2.86%	NA
Indica II	465	68.40%	18.90%	4.30%	8.39%	NA
Indica III	913	62.80%	24.00%	2.08%	11.17%	NA
Indica Intermediate	786	65.40%	29.90%	2.29%	2.42%	NA
Temperate Japonica	767	85.00%	3.70%	3.91%	7.43%	NA
Tropical Japonica	504	50.80%	1.80%	5.16%	42.26%	NA
Japonica Intermediate	241	80.90%	1.70%	2.90%	14.52%	NA
VI/Aromatic	96	92.70%	5.20%	2.08%	0.00%	NA
Intermediate	90	77.80%	11.10%	3.33%	7.78%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1000744795	G -> A	LOC_Os10g02170.1	upstream_gene_variant ; 2120.0bp to feature; MODIFIER	silent_mutation	Average:31.811; most accessible tissue: Callus, score: 84.785	N	N	N	N
vg1000744795	G -> A	LOC_Os10g02180.1	downstream_gene_variant ; 4607.0bp to feature; MODIFIER	silent_mutation	Average:31.811; most accessible tissue: Callus, score: 84.785	N	N	N	N
vg1000744795	G -> A	LOC_Os10g02170-LOC_Os10g02180	intergenic_region ; MODIFIER	silent_mutation	Average:31.811; most accessible tissue: Callus, score: 84.785	N	N	N	N
vg1000744795	G -> DEL	N	N	silent_mutation	Average:31.811; most accessible tissue: Callus, score: 84.785	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1000744795	2.35E-06	2.35E-06	mr1385	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
vg1000744795	NA	6.05E-08	mr1603	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