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Detailed information for vg0517271938:

Variant ID: vg0517271938 (JBrowse)	Variation Type: SNP
Chromosome: chr05	Position: 17271938
Reference Allele: C	Alternative Allele: T
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: 268. )

Flanking Sequence (100 bp) in Reference Genome:

TCTGGTTCGTGCTCTTCATGTCTTGGGCCCTCGTGTAGAATGTGTACCCATTGATTTCATATCCCTGGAATGTCGCGATCGAGCCAAATGGTCCCCTCGC[C/T]
AGGAAGGCCAGTTGTTGGTTAATCGTCTTGTTACCCATGAGATGTTGTTGCAGCCACATGGAGAAAGTATCAATGTGATGCCGTGTAATCCAAGCATCGG

Reverse complement sequence

CCGATGCTTGGATTACACGGCATCACATTGATACTTTCTCCATGTGGCTGCAACAACATCTCATGGGTAACAAGACGATTAACCAACAACTGGCCTTCCT[G/A]
GCGAGGGGACCATTTGGCTCGATCGCGACATTCCAGGGATATGAAATCAATGGGTACACATTCTACACGAGGGCCCAAGACATGAAGAGCACGAACCAGA

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	92.80%	7.10%	0.06%	0.00%	NA
All Indica	2759	93.90%	6.00%	0.11%	0.00%	NA
All Japonica	1512	99.80%	0.20%	0.00%	0.00%	NA
Aus	269	42.00%	58.00%	0.00%	0.00%	NA
Indica I	595	99.00%	0.70%	0.34%	0.00%	NA
Indica II	465	78.90%	21.10%	0.00%	0.00%	NA
Indica III	913	97.20%	2.80%	0.00%	0.00%	NA
Indica Intermediate	786	95.00%	4.80%	0.13%	0.00%	NA
Temperate Japonica	767	100.00%	0.00%	0.00%	0.00%	NA
Tropical Japonica	504	99.60%	0.40%	0.00%	0.00%	NA
Japonica Intermediate	241	99.60%	0.40%	0.00%	0.00%	NA
VI/Aromatic	96	93.80%	6.20%	0.00%	0.00%	NA
Intermediate	90	94.40%	5.60%	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
vg0517271938	C -> T	LOC_Os05g29850.1	synonymous_variant ; p.Leu889Leu; LOW	synonymous_codon	Average:21.084; most accessible tissue: Minghui63 panicle, score: 38.588	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0517271938	4.39E-06	NA	mr1593_2	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
vg0517271938	NA	6.52E-06	mr1942_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