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Detailed information for vg0207077547:

Variant ID: vg0207077547 (JBrowse)	Variation Type: SNP
Chromosome: chr02	Position: 7077547
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

AATATACTACTAGTCATTCCTCGTAAACAAGCGATTTATTAATATTTATATTTCTCAATGCCCATGTAGCCAATCATGTGTGGAAGAATGAAGAGTCACG[C/T]
ATTAAATTCGAGAAAATCATTAAGAGGATAAGTTGTTGGATTGAAATATGCCTATCAAAAATAAAATTTTCAAATTTAAAAATATGACTATCAAAAGTAG

Reverse complement sequence

CTACTTTTGATAGTCATATTTTTAAATTTGAAAATTTTATTTTTGATAGGCATATTTCAATCCAACAACTTATCCTCTTAATGATTTTCTCGAATTTAAT[G/A]
CGTGACTCTTCATTCTTCCACACATGATTGGCTACATGGGCATTGAGAAATATAAATATTAATAAATCGCTTGTTTACGAGGAATGACTAGTAGTATATT

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	98.10%	1.20%	0.63%	0.00%	NA
All Indica	2759	100.00%	0.00%	0.04%	0.00%	NA
All Japonica	1512	94.20%	3.80%	1.92%	0.00%	NA
Aus	269	100.00%	0.00%	0.00%	0.00%	NA
Indica I	595	100.00%	0.00%	0.00%	0.00%	NA
Indica II	465	100.00%	0.00%	0.00%	0.00%	NA
Indica III	913	100.00%	0.00%	0.00%	0.00%	NA
Indica Intermediate	786	99.90%	0.00%	0.13%	0.00%	NA
Temperate Japonica	767	98.80%	0.40%	0.78%	0.00%	NA
Tropical Japonica	504	87.50%	10.30%	2.18%	0.00%	NA
Japonica Intermediate	241	93.80%	1.20%	4.98%	0.00%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	100.00%	0.00%	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
vg0207077547	C -> T	LOC_Os02g13290.1	upstream_gene_variant ; 1156.0bp to feature; MODIFIER	silent_mutation	Average:28.837; most accessible tissue: Minghui63 panicle, score: 42.799	N	N	N	N
vg0207077547	C -> T	LOC_Os02g13270-LOC_Os02g13290	intergenic_region ; MODIFIER	silent_mutation	Average:28.837; most accessible tissue: Minghui63 panicle, score: 42.799	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0207077547	4.13E-06	4.13E-06	mr1254	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
vg0207077547	NA	9.20E-08	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