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Detailed information for vg0223708173:

Variant ID: vg0223708173 (JBrowse)	Variation Type: SNP
Chromosome: chr02	Position: 23708173
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: 295. )

Flanking Sequence (100 bp) in Reference Genome:

CACTCGAGCTGTTAAACAGTTTCCCATCCTTAATCACTAATTTTCTAATGTCCAGTCCCTATTGTGGATCACAAGCTAGGTGAACAACTTACATTTGTTT[G/A]
GTGCCTACGCTTTCCGGATGATTGTACACCAGGTATGGACTATAGCGGGAATCCAGCTGGCTGACTTTATGTGCCCTTGCAACATCTAGTTTGCGAGCAT

Reverse complement sequence

ATGCTCGCAAACTAGATGTTGCAAGGGCACATAAAGTCAGCCAGCTGGATTCCCGCTATAGTCCATACCTGGTGTACAATCATCCGGAAAGCGTAGGCAC[C/T]
AAACAAATGTAAGTTGTTCACCTAGCTTGTGATCCACAATAGGGACTGGACATTAGAAAATTAGTGATTAAGGATGGGAAACTGTTTAACAGCTCGAGTG

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	83.00%	16.70%	0.02%	0.25%	NA
All Indica	2759	72.60%	27.00%	0.04%	0.36%	NA
All Japonica	1512	99.80%	0.10%	0.00%	0.07%	NA
Aus	269	85.10%	14.90%	0.00%	0.00%	NA
Indica I	595	71.60%	28.10%	0.17%	0.17%	NA
Indica II	465	86.00%	13.50%	0.00%	0.43%	NA
Indica III	913	59.40%	40.40%	0.00%	0.22%	NA
Indica Intermediate	786	80.90%	18.40%	0.00%	0.64%	NA
Temperate Japonica	767	100.00%	0.00%	0.00%	0.00%	NA
Tropical Japonica	504	99.80%	0.20%	0.00%	0.00%	NA
Japonica Intermediate	241	99.20%	0.40%	0.00%	0.41%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	94.40%	4.40%	0.00%	1.11%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0223708173	G -> A	LOC_Os02g39250.1	synonymous_variant ; p.Thr244Thr; LOW	synonymous_codon	Average:38.108; most accessible tissue: Zhenshan97 young leaf, score: 54.618	N	N	N	N
vg0223708173	G -> DEL	LOC_Os02g39250.1	N	frameshift_variant	Average:38.108; most accessible tissue: Zhenshan97 young leaf, score: 54.618	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0223708173	NA	7.20E-06	mr1795	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
vg0223708173	NA	9.71E-06	mr1929	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
vg0223708173	2.88E-06	8.61E-07	mr1063_2	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
vg0223708173	4.81E-06	NA	mr1161_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
vg0223708173	8.66E-06	NA	mr1183_2	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
vg0223708173	3.26E-06	NA	mr1183_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