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Detailed information for vg0308083667:

Variant ID: vg0308083667 (JBrowse)	Variation Type: SNP
Chromosome: chr03	Position: 8083667
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

AAACAAAACTACGCTAAGGAATCACTTTACATCCGCCCATGACCGTGAACACGGCTGTTCGAACAGTTTAATAACCTCTGCAGAGGGGGCACACTTTACC[C/T]
ACACGACATTACTAACCCAGATCACCCAGCCCGTGCAGAACAGCCACGTCTGGTGACCTTGAGGCTTTCATAACAAGGCATTTCGAGAGCCGACACAGGT

Reverse complement sequence

ACCTGTGTCGGCTCTCGAAATGCCTTGTTATGAAAGCCTCAAGGTCACCAGACGTGGCTGTTCTGCACGGGCTGGGTGATCTGGGTTAGTAATGTCGTGT[G/A]
GGTAAAGTGTGCCCCCTCTGCAGAGGTTATTAAACTGTTCGAACAGCCGTGTTCACGGTCATGGGCGGATGTAAAGTGATTCCTTAGCGTAGTTTTGTTT

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	95.20%	4.80%	0.06%	0.00%	NA
All Indica	2759	100.00%	0.00%	0.00%	0.00%	NA
All Japonica	1512	85.20%	14.60%	0.20%	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	99.90%	0.10%	0.00%	0.00%	NA
Indica Intermediate	786	100.00%	0.00%	0.00%	0.00%	NA
Temperate Japonica	767	95.60%	4.30%	0.13%	0.00%	NA
Tropical Japonica	504	87.70%	12.10%	0.20%	0.00%	NA
Japonica Intermediate	241	46.90%	52.70%	0.41%	0.00%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	95.60%	4.40%	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
vg0308083667	C -> T	LOC_Os03g14840.1	upstream_gene_variant ; 3494.0bp to feature; MODIFIER	silent_mutation	Average:41.009; most accessible tissue: Zhenshan97 root, score: 55.432	N	N	N	N
vg0308083667	C -> T	LOC_Os03g14820-LOC_Os03g14840	intergenic_region ; MODIFIER	silent_mutation	Average:41.009; most accessible tissue: Zhenshan97 root, score: 55.432	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0308083667	8.15E-07	8.15E-07	mr1370	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