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Detailed information for vg0905621224:

Variant ID: vg0905621224 (JBrowse)	Variation Type: SNP
Chromosome: chr09	Position: 5621224
Reference Allele: A	Alternative Allele: G
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.94, A: 0.07, others allele: 0.00, population size: 254. )

Flanking Sequence (100 bp) in Reference Genome:

GCCAACTGCATCCATGGCGCAAAGCATATACACGCCATGCTTCAGAGTGGTGCTATCTTCATCTTCCGGGCAATTGTAAACTCCATACTCCTGATCATGA[A/G]
GCTTGTGTGGATGATACTGGAAATCTGATGACTCTAACTCCTCATCAAAGCGATGACGAAGCTCTCCAATGGCCACCAAAGCTGCCTCCTGACAAGCATG

Reverse complement sequence

CATGCTTGTCAGGAGGCAGCTTTGGTGGCCATTGGAGAGCTTCGTCATCGCTTTGATGAGGAGTTAGAGTCATCAGATTTCCAGTATCATCCACACAAGC[T/C]
TCATGATCAGGAGTATGGAGTTTACAATTGCCCGGAAGATGAAGATAGCACCACTCTGAAGCATGGCGTGTATATGCTTTGCGCCATGGATGCAGTTGGC

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	69.70%	30.30%	0.02%	0.00%	NA
All Indica	2759	98.00%	2.00%	0.00%	0.00%	NA
All Japonica	1512	19.10%	80.90%	0.00%	0.00%	NA
Aus	269	91.40%	8.60%	0.00%	0.00%	NA
Indica I	595	99.00%	1.00%	0.00%	0.00%	NA
Indica II	465	99.40%	0.60%	0.00%	0.00%	NA
Indica III	913	97.70%	2.30%	0.00%	0.00%	NA
Indica Intermediate	786	96.90%	3.10%	0.00%	0.00%	NA
Temperate Japonica	767	10.40%	89.60%	0.00%	0.00%	NA
Tropical Japonica	504	18.50%	81.50%	0.00%	0.00%	NA
Japonica Intermediate	241	48.10%	51.90%	0.00%	0.00%	NA
VI/Aromatic	96	6.20%	92.70%	1.04%	0.00%	NA
Intermediate	90	52.20%	47.80%	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
vg0905621224	A -> G	LOC_Os09g10310.1	missense_variant ; p.Leu102Pro; MODERATE	nonsynonymous_codon ; L102P	Average:53.249; most accessible tissue: Zhenshan97 flag leaf, score: 68.25	unknown	unknown	TOLERATED	1.00

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0905621224	NA	3.25E-08	mr1299_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
vg0905621224	NA	6.64E-08	mr1645_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
vg0905621224	NA	1.01E-08	mr1700_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
vg0905621224	NA	9.04E-07	mr1727_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