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Detailed information for vg0905621505:

Variant ID: vg0905621505 (JBrowse)	Variation Type: SNP
Chromosome: chr09	Position: 5621505
Reference Allele: T	Alternative Allele: C
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, others allele: 0.00, population size: 272. )

Flanking Sequence (100 bp) in Reference Genome:

TATTCTCCTCATTGGGGTCATGGGGAATTTGGCGATACTCGGGGACAATGTTGTAGCCTACTTCAAATGCCATCATTCTCAGCTCCCTGACGAATCCTAC[T/C]
GCATCGATCAAGCTTTCTGGCATCTAAAGGAACACATAAAGGAGGAATTAATGCATATATTTAAGTTAGCTGCACAAGCTAGACTCAATTAATTTTGACC

Reverse complement sequence

GGTCAAAATTAATTGAGTCTAGCTTGTGCAGCTAACTTAAATATATGCATTAATTCCTCCTTTATGTGTTCCTTTAGATGCCAGAAAGCTTGATCGATGC[A/G]
GTAGGATTCGTCAGGGAGCTGAGAATGATGGCATTTGAAGTAGGCTACAACATTGTCCCCGAGTATCGCCAAATTCCCCATGACCCCAATGAGGAGAATA

Allele Frequencies:

Populations	Population Size	Frequency of C(primary allele)	Frequency of T(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	72.50%	27.50%	0.02%	0.00%	NA
All Indica	2759	98.50%	1.50%	0.00%	0.00%	NA
All Japonica	1512	20.30%	79.70%	0.00%	0.00%	NA
Aus	269	92.90%	7.10%	0.00%	0.00%	NA
Indica I	595	99.00%	1.00%	0.00%	0.00%	NA
Indica II	465	99.40%	0.60%	0.00%	0.00%	NA
Indica III	913	98.00%	2.00%	0.00%	0.00%	NA
Indica Intermediate	786	98.10%	1.90%	0.00%	0.00%	NA
Temperate Japonica	767	10.40%	89.60%	0.00%	0.00%	NA
Tropical Japonica	504	18.80%	81.20%	0.00%	0.00%	NA
Japonica Intermediate	241	54.80%	45.20%	0.00%	0.00%	NA
VI/Aromatic	96	97.90%	2.10%	0.00%	0.00%	NA
Intermediate	90	62.20%	36.70%	1.11%	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
vg0905621505	T -> C	LOC_Os09g10310.1	synonymous_variant ; p.Ala8Ala; LOW	synonymous_codon	Average:35.165; most accessible tissue: Callus, score: 57.912	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0905621505	NA	1.90E-21	mr1163	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