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Detailed information for vg0335314709:

Variant ID: vg0335314709 (JBrowse)	Variation Type: SNP
Chromosome: chr03	Position: 35314709
Reference Allele: T	Alternative Allele: C
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.97, T: 0.03, others allele: 0.00, population size: 291. )

Flanking Sequence (100 bp) in Reference Genome:

GTTGCAAGCTGGTTGCAATCTCCACCTCTGTAACAAACTCTTGTATTGCATCAACTGAAGGTTTCAGAATCTTTACAGCTGATAATGTGCCATCAAATAG[T/C]
TGTGCCTTGTAAACTTGGCTTGTTCCTCCCTTTCCAATTAACATATCTGCATTGGTGTAAAAGAAAATCAGCAGACAACTTTGCCAAAAAGCCTGTGAAT

Reverse complement sequence

ATTCACAGGCTTTTTGGCAAAGTTGTCTGCTGATTTTCTTTTACACCAATGCAGATATGTTAATTGGAAAGGGAGGAACAAGCCAAGTTTACAAGGCACA[A/G]
CTATTTGATGGCACATTATCAGCTGTAAAGATTCTGAAACCTTCAGTTGATGCAATACAAGAGTTTGTTACAGAGGTGGAGATTGCAACCAGCTTGCAAC

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	59.70%	40.20%	0.08%	0.00%	NA
All Indica	2759	37.90%	61.90%	0.14%	0.00%	NA
All Japonica	1512	97.40%	2.60%	0.00%	0.00%	NA
Aus	269	59.90%	40.10%	0.00%	0.00%	NA
Indica I	595	69.40%	30.30%	0.34%	0.00%	NA
Indica II	465	22.80%	76.80%	0.43%	0.00%	NA
Indica III	913	30.80%	69.20%	0.00%	0.00%	NA
Indica Intermediate	786	31.40%	68.60%	0.00%	0.00%	NA
Temperate Japonica	767	98.00%	2.00%	0.00%	0.00%	NA
Tropical Japonica	504	95.20%	4.80%	0.00%	0.00%	NA
Japonica Intermediate	241	99.60%	0.40%	0.00%	0.00%	NA
VI/Aromatic	96	97.90%	2.10%	0.00%	0.00%	NA
Intermediate	90	54.40%	45.60%	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
vg0335314709	T -> C	LOC_Os03g62340.1	synonymous_variant ; p.Gln611Gln; LOW	synonymous_codon	Average:63.601; most accessible tissue: Callus, score: 78.573	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0335314709	NA	4.09E-06	mr1168_2	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