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Detailed information for vg0509750750:

Variant ID: vg0509750750 (JBrowse)	Variation Type: SNP
Chromosome: chr05	Position: 9750750
Reference Allele: T	Alternative Allele: C
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 1.00, C: 0.00, others allele: 0.00, population size: 236. )

Flanking Sequence (100 bp) in Reference Genome:

GTTCAGCTAGATGTTCGATATAATTGTTTAGCCATGCTTAGAAACATTAGCACATGATTGGGATTACTAATGTTACACTACCACTTGTGATTATATTTAA[T/C]
GGTAGCTCATGATGGTCAATCATGATTGGTTAATTAATTACTGGCCGACTAAAACTTGACAATGGTGGGTTGTGAGCACATGGTTTTGAAGGTCGTGCTC

Reverse complement sequence

GAGCACGACCTTCAAAACCATGTGCTCACAACCCACCATTGTCAAGTTTTAGTCGGCCAGTAATTAATTAACCAATCATGATTGACCATCATGAGCTACC[A/G]
TTAAATATAATCACAAGTGGTAGTGTAACATTAGTAATCCCAATCATGTGCTAATGTTTCTAAGCATGGCTAAACAATTATATCGAACATCTAGCTGAAC

Allele Frequencies:

Populations	Population Size	Frequency of T(primary allele)	Frequency of C(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	83.00%	14.60%	1.80%	0.55%	NA
All Indica	2759	73.60%	22.80%	2.83%	0.72%	NA
All Japonica	1512	99.40%	0.40%	0.20%	0.00%	NA
Aus	269	83.60%	16.40%	0.00%	0.00%	NA
Indica I	595	86.10%	10.40%	3.53%	0.00%	NA
Indica II	465	72.00%	24.70%	3.23%	0.00%	NA
Indica III	913	67.80%	28.80%	1.20%	2.19%	NA
Indica Intermediate	786	72.00%	24.00%	3.94%	0.00%	NA
Temperate Japonica	767	99.30%	0.40%	0.26%	0.00%	NA
Tropical Japonica	504	99.60%	0.40%	0.00%	0.00%	NA
Japonica Intermediate	241	99.20%	0.40%	0.41%	0.00%	NA
VI/Aromatic	96	90.60%	2.10%	1.04%	6.25%	NA
Intermediate	90	85.60%	11.10%	3.33%	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
vg0509750750	T -> DEL	N	N	silent_mutation	Average:37.293; most accessible tissue: Zhenshan97 young leaf, score: 61.964	N	N	N	N
vg0509750750	T -> C	LOC_Os05g17080.1	upstream_gene_variant ; 62.0bp to feature; MODIFIER	silent_mutation	Average:37.293; most accessible tissue: Zhenshan97 young leaf, score: 61.964	N	N	N	N
vg0509750750	T -> C	LOC_Os05g17070.1	downstream_gene_variant ; 3361.0bp to feature; MODIFIER	silent_mutation	Average:37.293; most accessible tissue: Zhenshan97 young leaf, score: 61.964	N	N	N	N
vg0509750750	T -> C	LOC_Os05g17070-LOC_Os05g17080	intergenic_region ; MODIFIER	silent_mutation	Average:37.293; most accessible tissue: Zhenshan97 young leaf, score: 61.964	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0509750750	NA	4.23E-06	mr1897	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