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Detailed information for vg0307547080:

Variant ID: vg0307547080 (JBrowse)	Variation Type: SNP
Chromosome: chr03	Position: 7547080
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.90, T: 0.10, others allele: 0.00, population size: 81. )

Flanking Sequence (100 bp) in Reference Genome:

GAAACAATGTGAACATCTTGTTTGACTAGACACTTACTATAGCTTCGTATACTCGTTGATCTTCTGCATTTGGCATGAAGATTGTGCCATCATCATTCTT[C/T]
TGGTACTGGCCCTGGCCCAGTTCCTAGCCCGAGGGTGTGGGATATTGCCAAACACTAGCGGTGTGCACGATTCCTCCGCTTCTTCATCCTCACGCTGCCA

Reverse complement sequence

TGGCAGCGTGAGGATGAAGAAGCGGAGGAATCGTGCACACCGCTAGTGTTTGGCAATATCCCACACCCTCGGGCTAGGAACTGGGCCAGGGCCAGTACCA[G/A]
AAGAATGATGATGGCACAATCTTCATGCCAAATGCAGAAGATCAACGAGTATACGAAGCTATAGTAAGTGTCTAGTCAAACAAGATGTTCACATTGTTTC

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	28.60%	1.90%	1.93%	67.54%	NA
All Indica	2759	1.70%	3.00%	1.70%	93.66%	NA
All Japonica	1512	83.70%	0.10%	0.13%	16.01%	NA
Aus	269	1.10%	1.50%	10.04%	87.36%	NA
Indica I	595	2.50%	2.50%	1.85%	93.11%	NA
Indica II	465	1.50%	4.30%	1.94%	92.26%	NA
Indica III	913	0.90%	2.10%	1.20%	95.84%	NA
Indica Intermediate	786	2.00%	3.60%	2.04%	92.37%	NA
Temperate Japonica	767	80.10%	0.10%	0.00%	19.82%	NA
Tropical Japonica	504	83.70%	0.20%	0.20%	15.87%	NA
Japonica Intermediate	241	95.40%	0.00%	0.41%	4.15%	NA
VI/Aromatic	96	4.20%	4.20%	13.54%	78.12%	NA
Intermediate	90	35.60%	0.00%	2.22%	62.22%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0307547080	C -> T	LOC_Os03g13910.1	upstream_gene_variant ; 1934.0bp to feature; MODIFIER	silent_mutation	Average:27.982; most accessible tissue: Minghui63 root, score: 35.002	N	N	N	N
vg0307547080	C -> T	LOC_Os03g13920.1	downstream_gene_variant ; 161.0bp to feature; MODIFIER	silent_mutation	Average:27.982; most accessible tissue: Minghui63 root, score: 35.002	N	N	N	N
vg0307547080	C -> T	LOC_Os03g13910-LOC_Os03g13920	intergenic_region ; MODIFIER	silent_mutation	Average:27.982; most accessible tissue: Minghui63 root, score: 35.002	N	N	N	N
vg0307547080	C -> DEL	N	N	silent_mutation	Average:27.982; most accessible tissue: Minghui63 root, score: 35.002	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0307547080	4.07E-06	NA	mr1672_2	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