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Detailed information for vg1200180797:

Variant ID: vg1200180797 (JBrowse)	Variation Type: SNP
Chromosome: chr12	Position: 180797
Reference Allele: T	Alternative Allele: C,A
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.86, C: 0.14, others allele: 0.00, population size: 74. )

Flanking Sequence (100 bp) in Reference Genome:

ACTTTACAATCAGGGATGGGGGATGCTTGGAATTTTATCTGGGACTCAGATAAGTACACAGCTAAGAAATTCTATAAGCTAAATTATTCTGCATTGCAAC[T/C,A]
CCCCAGGCCCATGATTTGGCTATGGAAAACAAAATGTGTCATGAAGATCAAAGTCTTTGCCTGGCTAATGTTCTGTGATAGGCTCAATACAAGAGATATG

Reverse complement sequence

CATATCTCTTGTATTGAGCCTATCACAGAACATTAGCCAGGCAAAGACTTTGATCTTCATGACACATTTTGTTTTCCATAGCCAAATCATGGGCCTGGGG[A/G,T]
GTTGCAATGCAGAATAATTTAGCTTATAGAATTTCTTAGCTGTGTACTTATCTGAGTCCCAGATAAAATTCCAAGCATCCCCCATCCCTGATTGTAAAGT

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	50.50%	47.40%	1.33%	0.78%	NA
All Indica	2759	79.70%	18.20%	1.70%	0.40%	NA
All Japonica	1512	2.20%	96.00%	0.13%	1.59%	NA
Aus	269	44.20%	51.70%	4.09%	0.00%	NA
Indica I	595	77.10%	20.20%	1.85%	0.84%	NA
Indica II	465	84.90%	13.10%	0.86%	1.08%	NA
Indica III	913	80.00%	18.80%	1.20%	0.00%	NA
Indica Intermediate	786	78.40%	18.80%	2.67%	0.13%	NA
Temperate Japonica	767	3.30%	94.50%	0.00%	2.22%	NA
Tropical Japonica	504	1.20%	97.40%	0.20%	1.19%	NA
Japonica Intermediate	241	1.20%	97.90%	0.41%	0.41%	NA
VI/Aromatic	96	3.10%	93.80%	2.08%	1.04%	NA
Intermediate	90	32.20%	65.60%	1.11%	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
vg1200180797	T -> C	LOC_Os12g01320.1	missense_variant ; p.Leu362Pro; MODERATE	nonsynonymous_codon ; L362P	Average:13.963; most accessible tissue: Callus, score: 35.887	unknown	unknown	TOLERATED	0.47
vg1200180797	T -> DEL	LOC_Os12g01320.1	N	frameshift_variant	Average:13.963; most accessible tissue: Callus, score: 35.887	N	N	N	N
vg1200180797	T -> A	LOC_Os12g01320.1	missense_variant ; p.Leu362His; MODERATE	N	Average:13.963; most accessible tissue: Callus, score: 35.887	N	N	N	N
vg1200180797	T -> A	LOC_Os12g01310.1	upstream_gene_variant ; 2921.0bp to feature; MODIFIER	N	Average:13.963; most accessible tissue: Callus, score: 35.887	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1200180797	NA	2.32E-21	mr1021	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
vg1200180797	NA	2.59E-06	mr1029	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
vg1200180797	NA	4.20E-14	mr1032	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
vg1200180797	NA	4.06E-09	mr1047	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
vg1200180797	NA	2.36E-17	mr1165	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
vg1200180797	NA	7.75E-09	mr1174	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
vg1200180797	NA	3.89E-06	mr1189	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
vg1200180797	NA	4.62E-06	mr1216	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
vg1200180797	NA	4.31E-16	mr1323	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
vg1200180797	NA	2.14E-11	mr1325	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
vg1200180797	NA	2.77E-13	mr1326	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
vg1200180797	NA	3.55E-06	mr1336	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
vg1200180797	7.89E-06	4.82E-07	mr1448	Ind_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
vg1200180797	NA	9.31E-22	mr1477	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
vg1200180797	NA	1.07E-14	mr1478	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
vg1200180797	NA	3.86E-06	mr1532	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
vg1200180797	NA	7.14E-06	mr1625	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
vg1200180797	NA	6.66E-13	mr1744	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
vg1200180797	NA	9.19E-08	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
vg1200180797	NA	6.35E-06	mr1782	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
vg1200180797	NA	6.48E-07	mr1796	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
vg1200180797	NA	2.20E-21	mr1971	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
vg1200180797	NA	9.22E-07	mr1990	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
vg1200180797	NA	5.32E-27	mr1270_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
vg1200180797	NA	6.68E-25	mr1316_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