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Detailed information for vg1206442588:

Variant ID: vg1206442588 (JBrowse)	Variation Type: SNP
Chromosome: chr12	Position: 6442588
Reference Allele: C	Alternative Allele: T
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.70, C: 0.29, others allele: 0.00, population size: 78. )

Flanking Sequence (100 bp) in Reference Genome:

TCCTCAACCACCATATGGACTTACCTATAAGCCACTGGAGAAAGACGGTGGAGAGAGGTGGGGCCCACGGTTTGACCGAACTAGGGGTTCAACCGAACCG[C/T]
CACTGGCCCCCCTCGTCTGCACCTTACACGTGTAGGCTCCCGAAGCTCTCCCAATGATAGTTGTGGAGGAGTGAGCCCCATTCTTCTCAACCGTCATAGC

Reverse complement sequence

GCTATGACGGTTGAGAAGAATGGGGCTCACTCCTCCACAACTATCATTGGGAGAGCTTCGGGAGCCTACACGTGTAAGGTGCAGACGAGGGGGGCCAGTG[G/A]
CGGTTCGGTTGAACCCCTAGTTCGGTCAAACCGTGGGCCCCACCTCTCTCCACCGTCTTTCTCCAGTGGCTTATAGGTAAGTCCATATGGTGGTTGAGGA

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	25.70%	16.30%	0.21%	57.79%	NA
All Indica	2759	36.90%	7.10%	0.14%	55.78%	NA
All Japonica	1512	6.30%	32.10%	0.26%	61.38%	NA
Aus	269	2.20%	21.90%	0.37%	75.46%	NA
Indica I	595	87.10%	4.40%	0.00%	8.57%	NA
Indica II	465	21.30%	16.80%	0.86%	61.08%	NA
Indica III	913	11.30%	2.60%	0.00%	86.09%	NA
Indica Intermediate	786	38.00%	8.80%	0.00%	53.18%	NA
Temperate Japonica	767	9.30%	42.20%	0.26%	48.24%	NA
Tropical Japonica	504	3.00%	11.70%	0.40%	84.92%	NA
Japonica Intermediate	241	3.70%	42.30%	0.00%	53.94%	NA
VI/Aromatic	96	68.80%	10.40%	0.00%	20.83%	NA
Intermediate	90	30.00%	23.30%	1.11%	45.56%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1206442588	C -> DEL	N	N	silent_mutation	Average:64.866; most accessible tissue: Minghui63 young leaf, score: 77.654	N	N	N	N
vg1206442588	C -> T	LOC_Os12g11860.1	upstream_gene_variant ; 4670.0bp to feature; MODIFIER	silent_mutation	Average:64.866; most accessible tissue: Minghui63 young leaf, score: 77.654	N	N	N	N
vg1206442588	C -> T	LOC_Os12g11840-LOC_Os12g11860	intergenic_region ; MODIFIER	silent_mutation	Average:64.866; most accessible tissue: Minghui63 young leaf, score: 77.654	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1206442588	5.15E-06	5.15E-06	mr1173	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
vg1206442588	4.15E-06	4.15E-06	mr1261	Jap_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
vg1206442588	1.02E-06	1.02E-06	mr1381	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
vg1206442588	NA	6.27E-06	mr1923_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