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Detailed information for vg0514322241:

Variant ID: vg0514322241 (JBrowse)	Variation Type: SNP
Chromosome: chr05	Position: 14322241
Reference Allele: T	Alternative Allele: C
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.93, C: 0.08, others allele: 0.00, population size: 272. )

Flanking Sequence (100 bp) in Reference Genome:

TTCGCAATAATGCACCCGGCCACAAATTTGTCGGGTAAGACACACTTAAGGAGTTCGAGTTCCTTAGCTATGGTTTGTATCTCATGAGCCTGTTCGACTA[T/C]
AGAACGGTTGTCAGCTATCCTATAGTCATGAAACTGCTCCATGATGTATAGATCATTGCTAGCATTAGTAGCAACGAATTTAGTATTCAGTGCATCCCAC

Reverse complement sequence

GTGGGATGCACTGAATACTAAATTCGTTGCTACTAATGCTAGCAATGATCTATACATCATGGAGCAGTTTCATGACTATAGGATAGCTGACAACCGTTCT[A/G]
TAGTCGAACAGGCTCATGAGATACAAACCATAGCTAAGGAACTCGAACTCCTTAAGTGTGTCTTACCCGACAAATTTGTGGCCGGGTGCATTATTGCGAA

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	85.50%	13.50%	0.95%	0.00%	NA
All Indica	2759	83.50%	14.90%	1.63%	0.00%	NA
All Japonica	1512	99.80%	0.20%	0.00%	0.00%	NA
Aus	269	20.40%	79.60%	0.00%	0.00%	NA
Indica I	595	96.60%	1.20%	2.18%	0.00%	NA
Indica II	465	74.60%	22.40%	3.01%	0.00%	NA
Indica III	913	73.50%	26.00%	0.55%	0.00%	NA
Indica Intermediate	786	90.30%	8.00%	1.65%	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	99.60%	0.40%	0.00%	0.00%	NA
VI/Aromatic	96	99.00%	1.00%	0.00%	0.00%	NA
Intermediate	90	90.00%	10.00%	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
vg0514322241	T -> C	LOC_Os05g24710.1	missense_variant ; p.Ile89Val; MODERATE	nonsynonymous_codon ; I89V	Average:54.114; most accessible tissue: Zhenshan97 flag leaf, score: 69.582	benign	-0.392	TOLERATED	1.00

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0514322241	1.86E-07	NA	mr1039	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
vg0514322241	9.33E-06	8.60E-17	mr1039	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
vg0514322241	NA	4.61E-09	mr1632	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
vg0514322241	3.70E-12	NA	mr1039_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
vg0514322241	3.20E-09	5.53E-21	mr1039_2	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
vg0514322241	NA	4.44E-06	mr1158_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
vg0514322241	NA	3.21E-06	mr1514_2	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
vg0514322241	2.73E-11	NA	mr1632_2	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
vg0514322241	4.27E-09	9.37E-18	mr1632_2	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