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Detailed information for vg0207655807:

Variant ID: vg0207655807 (JBrowse)	Variation Type: SNP
Chromosome: chr02	Position: 7655807
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

TCAATCCTAGTCAAGGTTTGTAAGGAATGTGTTTTTATGGAAACTCCGTTCGTAGGACTACCTTGCATGACGCCGTTAATTTTTGTGTTTGACGTTTGAC[C/T]
ATTCGTCTTATGTAAAAAATTTATATAATTATCATTTATTTTAATGTGACTTGATTCATTAAATGTTCTTTAAGCATGGCATAAATATTTTTATATTTAC

Reverse complement sequence

GTAAATATAAAAATATTTATGCCATGCTTAAAGAACATTTAATGAATCAAGTCACATTAAAATAAATGATAATTATATAAATTTTTTACATAAGACGAAT[G/A]
GTCAAACGTCAAACACAAAAATTAACGGCGTCATGCAAGGTAGTCCTACGAACGGAGTTTCCATAAAAACACATTCCTTACAAACCTTGACTAGGATTGA

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	93.70%	5.70%	0.53%	0.00%	NA
All Indica	2759	98.40%	1.50%	0.14%	0.00%	NA
All Japonica	1512	99.10%	0.40%	0.46%	0.00%	NA
Aus	269	36.80%	58.70%	4.46%	0.00%	NA
Indica I	595	99.80%	0.20%	0.00%	0.00%	NA
Indica II	465	98.90%	1.10%	0.00%	0.00%	NA
Indica III	913	98.00%	2.00%	0.00%	0.00%	NA
Indica Intermediate	786	97.30%	2.20%	0.51%	0.00%	NA
Temperate Japonica	767	98.70%	0.40%	0.91%	0.00%	NA
Tropical Japonica	504	100.00%	0.00%	0.00%	0.00%	NA
Japonica Intermediate	241	98.80%	1.20%	0.00%	0.00%	NA
VI/Aromatic	96	41.70%	56.20%	2.08%	0.00%	NA
Intermediate	90	86.70%	13.30%	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
vg0207655807	C -> T	LOC_Os02g14020.1	downstream_gene_variant ; 176.0bp to feature; MODIFIER	silent_mutation	Average:91.693; most accessible tissue: Callus, score: 95.617	N	N	N	N
vg0207655807	C -> T	LOC_Os02g14030.1	downstream_gene_variant ; 2894.0bp to feature; MODIFIER	silent_mutation	Average:91.693; most accessible tissue: Callus, score: 95.617	N	N	N	N
vg0207655807	C -> T	LOC_Os02g14020-LOC_Os02g14030	intergenic_region ; MODIFIER	silent_mutation	Average:91.693; most accessible tissue: Callus, score: 95.617	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0207655807	NA	5.04E-07	mr1530	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
vg0207655807	NA	8.29E-10	mr1570	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
vg0207655807	NA	8.29E-06	mr1684	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
vg0207655807	NA	2.39E-06	mr1803	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
vg0207655807	NA	9.61E-07	mr1808	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
vg0207655807	NA	1.51E-08	mr1126_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
vg0207655807	NA	1.15E-09	mr1166_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
vg0207655807	NA	8.90E-08	mr1465_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
vg0207655807	NA	2.01E-09	mr1567_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
vg0207655807	NA	1.80E-08	mr1582_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
vg0207655807	NA	5.31E-10	mr1612_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
vg0207655807	2.43E-06	NA	mr1711_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
vg0207655807	NA	2.49E-08	mr1735_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
vg0207655807	NA	5.37E-08	mr1765_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