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Detailed information for vg1005761243:

Variant ID: vg1005761243 (JBrowse)	Variation Type: SNP
Chromosome: chr10	Position: 5761243
Reference Allele: T	Alternative Allele: C
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 1.00, others allele: 0.00, population size: 322. )

Flanking Sequence (100 bp) in Reference Genome:

GCAGATCATGTGCTGGGGGTACAAGACGATGTTATCTTAGACGCTAAATCCTATTTTGATGAGTTGCATAGTATTTTCCCTGGGAAGAATGTGCTGGACA[T/C]
TGAAGGTCACAATGGAGGAAGAAGAACAGATGACGATGGCTATGAGGGTCTGGTGATGGCTGCTGGCAAGGGCTTCCGGTTATGCCTTGATTTTCTGACA

Reverse complement sequence

TGTCAGAAAATCAAGGCATAACCGGAAGCCCTTGCCAGCAGCCATCACCAGACCCTCATAGCCATCGTCATCTGTTCTTCTTCCTCCATTGTGACCTTCA[A/G]
TGTCCAGCACATTCTTCCCAGGGAAAATACTATGCAACTCATCAAAATAGGATTTAGCGTCTAAGATAACATCGTCTTGTACCCCCAGCACATGATCTGC

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	91.00%	5.80%	3.15%	0.00%	NA
All Indica	2759	85.20%	9.70%	5.15%	0.00%	NA
All Japonica	1512	99.60%	0.30%	0.13%	0.00%	NA
Aus	269	99.60%	0.40%	0.00%	0.00%	NA
Indica I	595	76.60%	9.10%	14.29%	0.00%	NA
Indica II	465	74.60%	20.20%	5.16%	0.00%	NA
Indica III	913	91.10%	8.20%	0.66%	0.00%	NA
Indica Intermediate	786	91.00%	5.60%	3.44%	0.00%	NA
Temperate Japonica	767	99.60%	0.30%	0.13%	0.00%	NA
Tropical Japonica	504	99.80%	0.00%	0.20%	0.00%	NA
Japonica Intermediate	241	99.20%	0.80%	0.00%	0.00%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	90.00%	4.40%	5.56%	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
vg1005761243	T -> C	LOC_Os10g10480.1	missense_variant ; p.Ile223Thr; MODERATE	nonsynonymous_codon ; I223T	Average:73.114; most accessible tissue: Minghui63 panicle, score: 86.85	unknown	unknown	DELETERIOUS	0.04

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1005761243	NA	7.84E-07	mr1053	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
vg1005761243	4.27E-06	9.39E-09	mr1053_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
vg1005761243	NA	3.87E-07	mr1053_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
vg1005761243	NA	2.26E-06	mr1250_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