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Detailed information for vg0800289042:

Variant ID: vg0800289042 (JBrowse)	Variation Type: SNP
Chromosome: chr08	Position: 289042
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.88, T: 0.13, others allele: 0.00, population size: 254. )

Flanking Sequence (100 bp) in Reference Genome:

AGTTCATACCTGGGCATATCCTCCGACCAGTTCCGAATGGCAAGAAATTGAAATTATTTCCATTGTACCCAGCCATTGTGTTGCTAAGGAACCTCTCTGG[C/T]
ATGAACTCCTCGGCATTTTCCCAATAGCTAGGGTCCCTGGCAATAGCCCATGCATTGACGATGACACGAGTGCCTGAGGGTATAGTATAGCCCTCAACAT

Reverse complement sequence

ATGTTGAGGGCTATACTATACCCTCAGGCACTCGTGTCATCGTCAATGCATGGGCTATTGCCAGGGACCCTAGCTATTGGGAAAATGCCGAGGAGTTCAT[G/A]
CCAGAGAGGTTCCTTAGCAACACAATGGCTGGGTACAATGGAAATAATTTCAATTTCTTGCCATTCGGAACTGGTCGGAGGATATGCCCAGGTATGAACT

Allele Frequencies:

Populations	Population Size	Frequency of C(primary allele)	Frequency of T(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	57.30%	42.50%	0.17%	0.11%	NA
All Indica	2759	41.20%	58.40%	0.29%	0.14%	NA
All Japonica	1512	87.50%	12.50%	0.00%	0.00%	NA
Aus	269	65.40%	34.60%	0.00%	0.00%	NA
Indica I	595	57.80%	41.70%	0.34%	0.17%	NA
Indica II	465	23.90%	75.90%	0.22%	0.00%	NA
Indica III	913	37.80%	61.70%	0.33%	0.22%	NA
Indica Intermediate	786	42.90%	56.70%	0.25%	0.13%	NA
Temperate Japonica	767	97.40%	2.60%	0.00%	0.00%	NA
Tropical Japonica	504	71.60%	28.40%	0.00%	0.00%	NA
Japonica Intermediate	241	89.20%	10.80%	0.00%	0.00%	NA
VI/Aromatic	96	16.70%	83.30%	0.00%	0.00%	NA
Intermediate	90	60.00%	38.90%	0.00%	1.11%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0800289042	C -> T	LOC_Os08g01450.1	missense_variant ; p.Met420Ile; MODERATE	nonsynonymous_codon ; M420I	Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125	benign	0.291	TOLERATED	0.40
vg0800289042	C -> DEL	LOC_Os08g01450.1	N	frameshift_variant	Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0800289042	3.10E-08	1.87E-13	mr1277	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
vg0800289042	1.14E-08	8.10E-08	mr1277	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
vg0800289042	1.38E-24	1.66E-50	mr1746	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
vg0800289042	1.20E-20	5.22E-27	mr1746	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
vg0800289042	NA	2.12E-11	mr1746	Jap_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
vg0800289042	9.97E-11	1.27E-14	mr1277_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
vg0800289042	1.85E-10	1.66E-07	mr1277_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
vg0800289042	1.66E-06	NA	mr1298_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
vg0800289042	NA	9.06E-06	mr1582_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
vg0800289042	NA	1.47E-06	mr1632_2	Jap_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
vg0800289042	NA	2.68E-07	mr1676_2	Jap_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
vg0800289042	1.93E-30	1.32E-64	mr1746_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
vg0800289042	8.72E-27	1.96E-37	mr1746_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
vg0800289042	NA	6.01E-10	mr1746_2	Jap_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