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Detailed information for vg0601262655:

Variant ID: vg0601262655 (JBrowse)	Variation Type: SNP
Chromosome: chr06	Position: 1262655
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.00, others allele: 0.00, population size: 254. )

Flanking Sequence (100 bp) in Reference Genome:

GTATGGCTTGTCTTCGGTCTGGTGCAAATCTCCGCAGTCTTTGCTTTACTGGCTTGGCATCGGGTCGCACCATGAGTTTGTGCTCGATCACCTCCCTGGG[G/A]
ACCCCCGGCATGTCGGACGGCTGCCAAGCGAACACGTCGGCATTGTCGTGGAGGAAGGTGATGAGCGCGAGTTCCTATTTCTCGTTTAGTGATGCCCTGA

Reverse complement sequence

TCAGGGCATCACTAAACGAGAAATAGGAACTCGCGCTCATCACCTTCCTCCACGACAATGCCGACGTGTTCGCTTGGCAGCCGTCCGACATGCCGGGGGT[C/T]
CCCAGGGAGGTGATCGAGCACAAACTCATGGTGCGACCCGATGCCAAGCCAGTAAAGCAAAGACTGCGGAGATTTGCACCAGACCGAAGACAAGCCATAC

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	91.00%	8.80%	0.13%	0.00%	NA
All Indica	2759	88.50%	11.30%	0.14%	0.00%	NA
All Japonica	1512	99.70%	0.30%	0.00%	0.00%	NA
Aus	269	80.70%	19.00%	0.37%	0.00%	NA
Indica I	595	94.30%	5.70%	0.00%	0.00%	NA
Indica II	465	94.80%	4.90%	0.22%	0.00%	NA
Indica III	913	81.90%	18.10%	0.00%	0.00%	NA
Indica Intermediate	786	88.00%	11.60%	0.38%	0.00%	NA
Temperate Japonica	767	99.90%	0.10%	0.00%	0.00%	NA
Tropical Japonica	504	99.80%	0.20%	0.00%	0.00%	NA
Japonica Intermediate	241	99.20%	0.80%	0.00%	0.00%	NA
VI/Aromatic	96	53.10%	45.80%	1.04%	0.00%	NA
Intermediate	90	93.30%	6.70%	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
vg0601262655	G -> A	LOC_Os06g03310.1	synonymous_variant ; p.Val4Val; LOW	synonymous_codon	Average:37.437; most accessible tissue: Minghui63 young leaf, score: 61.007	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0601262655	NA	2.36E-06	mr1125	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
vg0601262655	NA	1.31E-06	mr1344	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
vg0601262655	1.80E-06	3.15E-07	mr1448	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