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Detailed information for vg0207433349:

Variant ID: vg0207433349 (JBrowse)	Variation Type: SNP
Chromosome: chr02	Position: 7433349
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: 277. )

Flanking Sequence (100 bp) in Reference Genome:

CTGCATACCATATTGAAGAGGAGGAGCAGAGCAATTGTCAGCCAAGTGACTACAAGGAGTTGTTCAACCTTCGTCACTCAAAGCTGCGCAACAACATAAA[G/A]
CGTGCCACAGCGCTATTGAAGATGAGGTTCCCAATTTTAAATGTCGCAACATTCTATCAGATAGAAACTCAAGCGAAAATCCCAGCAGCAGCAGTGGTGC

Reverse complement sequence

GCACCACTGCTGCTGCTGGGATTTTCGCTTGAGTTTCTATCTGATAGAATGTTGCGACATTTAAAATTGGGAACCTCATCTTCAATAGCGCTGTGGCACG[C/T]
TTTATGTTGTTGCGCAGCTTTGAGTGACGAAGGTTGAACAACTCCTTGTAGTCACTTGGCTGACAATTGCTCTGCTCCTCCTCTTCAATATGGTATGCAG

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	50.30%	39.70%	0.42%	9.59%	NA
All Indica	2759	17.70%	66.30%	0.69%	15.26%	NA
All Japonica	1512	97.60%	1.40%	0.00%	0.99%	NA
Aus	269	99.30%	0.70%	0.00%	0.00%	NA
Indica I	595	9.70%	61.50%	1.34%	27.39%	NA
Indica II	465	14.60%	59.10%	0.22%	26.02%	NA
Indica III	913	23.50%	74.90%	0.22%	1.31%	NA
Indica Intermediate	786	18.80%	64.20%	1.02%	15.90%	NA
Temperate Japonica	767	98.20%	0.50%	0.00%	1.30%	NA
Tropical Japonica	504	96.40%	3.40%	0.00%	0.20%	NA
Japonica Intermediate	241	98.30%	0.00%	0.00%	1.66%	NA
VI/Aromatic	96	97.90%	2.10%	0.00%	0.00%	NA
Intermediate	90	55.60%	24.40%	1.11%	18.89%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0207433349	G -> A	LOC_Os02g13770.1	synonymous_variant ; p.Lys291Lys; LOW	synonymous_codon	Average:71.674; most accessible tissue: Zhenshan97 young leaf, score: 81.102	N	N	N	N
vg0207433349	G -> DEL	LOC_Os02g13770.1	N	frameshift_variant	Average:71.674; most accessible tissue: Zhenshan97 young leaf, score: 81.102	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0207433349	2.12E-06	NA	mr1068	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
vg0207433349	8.61E-06	NA	mr1234	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
vg0207433349	4.48E-06	NA	mr1234	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
vg0207433349	NA	1.97E-30	mr1237	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
vg0207433349	NA	4.57E-15	mr1261	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
vg0207433349	NA	3.32E-11	mr1883	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