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Detailed information for vg0903742384:

Variant ID: vg0903742384 (JBrowse)	Variation Type: SNP
Chromosome: chr09	Position: 3742384
Reference Allele: G	Alternative Allele: A
Primary Allele: A	Secondary Allele: G

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.78, A: 0.21, others allele: 0.00, population size: 227. )

Flanking Sequence (100 bp) in Reference Genome:

AAGGTTACTGGGTCGAACGGAGTTTACCTCAGTAGAGAGTTGACCACGCACGGTGAAGTGTTTGGCAGGAGTTCGAACCGGCTCGACTGGTTCACGTGGT[G/A]
GAACAGGAGCTCGCGGTTCATCTCCAAAACGAATCTCGCCCTCTTCGTGTATGTCCTCGACGACTCTTTCGATCACATTCACTTCGCATGGGGAGTTGGA

Reverse complement sequence

TCCAACTCCCCATGCGAAGTGAATGTGATCGAAAGAGTCGTCGAGGACATACACGAAGAGGGCGAGATTCGTTTTGGAGATGAACCGCGAGCTCCTGTTC[C/T]
ACCACGTGAACCAGTCGAGCCGGTTCGAACTCCTGCCAAACACTTCACCGTGCGTGGTCAACTCTCTACTGAGGTAAACTCCGTTCGACCCAGTAACCTT

Allele Frequencies:

Populations	Population Size	Frequency of A(primary allele)	Frequency of G(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	62.10%	37.90%	0.02%	0.00%	NA
All Indica	2759	94.60%	5.40%	0.00%	0.00%	NA
All Japonica	1512	0.90%	99.10%	0.00%	0.00%	NA
Aus	269	99.30%	0.70%	0.00%	0.00%	NA
Indica I	595	94.60%	5.40%	0.00%	0.00%	NA
Indica II	465	92.00%	8.00%	0.00%	0.00%	NA
Indica III	913	97.40%	2.60%	0.00%	0.00%	NA
Indica Intermediate	786	92.90%	7.10%	0.00%	0.00%	NA
Temperate Japonica	767	0.80%	99.20%	0.00%	0.00%	NA
Tropical Japonica	504	1.00%	99.00%	0.00%	0.00%	NA
Japonica Intermediate	241	1.20%	98.80%	0.00%	0.00%	NA
VI/Aromatic	96	6.20%	93.80%	0.00%	0.00%	NA
Intermediate	90	41.10%	57.80%	1.11%	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
vg0903742384	G -> A	LOC_Os09g07470.1	missense_variant ; p.Pro85Leu; MODERATE	nonsynonymous_codon ; P85L	Average:66.251; most accessible tissue: Zhenshan97 young leaf, score: 83.199	unknown	unknown	TOLERATED	0.42

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0903742384	NA	6.90E-07	mr1781	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
vg0903742384	NA	6.66E-10	mr1756_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