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Detailed information for vg0905621113:

Variant ID: vg0905621113 (JBrowse)	Variation Type: SNP
Chromosome: chr09	Position: 5621113
Reference Allele: C	Alternative Allele: T
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 1.00, C: 0.00, others allele: 0.00, population size: 304. )

Flanking Sequence (100 bp) in Reference Genome:

TCCCTTGAGCTCGGCCAGTTCCTTCTGCAGGCGATACACCTTGCTTTCTAGCTTGCAAATCTTGCGACGGTTCCAATTTTCCCTCTCATGAGCTGCTTTC[C/T]
GCCGCTCCACGCCAACTGCATCCATGGCGCAAAGCATATACACGCCATGCTTCAGAGTGGTGCTATCTTCATCTTCCGGGCAATTGTAAACTCCATACTC

Reverse complement sequence

GAGTATGGAGTTTACAATTGCCCGGAAGATGAAGATAGCACCACTCTGAAGCATGGCGTGTATATGCTTTGCGCCATGGATGCAGTTGGCGTGGAGCGGC[G/A]
GAAAGCAGCTCATGAGAGGGAAAATTGGAACCGTCGCAAGATTTGCAAGCTAGAAAGCAAGGTGTATCGCCTGCAGAAGGAACTGGCCGAGCTCAAGGGA

Allele Frequencies:

Populations	Population Size	Frequency of T(primary allele)	Frequency of C(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	72.50%	27.50%	0.00%	0.00%	NA
All Indica	2759	98.40%	1.60%	0.00%	0.00%	NA
All Japonica	1512	20.30%	79.70%	0.00%	0.00%	NA
Aus	269	92.90%	7.10%	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	98.00%	2.00%	0.00%	0.00%	NA
Indica Intermediate	786	98.00%	2.00%	0.00%	0.00%	NA
Temperate Japonica	767	10.40%	89.60%	0.00%	0.00%	NA
Tropical Japonica	504	18.80%	81.20%	0.00%	0.00%	NA
Japonica Intermediate	241	54.80%	45.20%	0.00%	0.00%	NA
VI/Aromatic	96	97.90%	2.10%	0.00%	0.00%	NA
Intermediate	90	63.30%	36.70%	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
vg0905621113	C -> T	LOC_Os09g10310.1	missense_variant ; p.Arg139Gln; MODERATE	nonsynonymous_codon ; R139Q	Average:53.943; most accessible tissue: Zhenshan97 flag leaf, score: 70.425	unknown	unknown	TOLERATED	0.27

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0905621113	NA	1.78E-22	mr1163	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
vg0905621113	NA	7.21E-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