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Detailed information for vg0914999957:

Variant ID: vg0914999957 (JBrowse)	Variation Type: SNP
Chromosome: chr09	Position: 14999957
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

GTCAGGTGCCAAGTCCCGCCGGACGATAAAAAAAGTAGAAAAGGTAAAAGGTGGCGATGCGCCGAATTGTATTGATCGTGAGGATAGATTACATAGACCC[C/T]
GGGTGTACATATTTATACCCACGGGTTGATACAAGTCCTTGTCGGACAAGAAAGAAACTTTCCTAAATATAAAAAGAAAAGATAAAGTCCTTATAGGACA

Reverse complement sequence

TGTCCTATAAGGACTTTATCTTTTCTTTTTATATTTAGGAAAGTTTCTTTCTTGTCCGACAAGGACTTGTATCAACCCGTGGGTATAAATATGTACACCC[G/A]
GGGTCTATGTAATCTATCCTCACGATCAATACAATTCGGCGCATCGCCACCTTTTACCTTTTCTACTTTTTTTATCGTCCGGCGGGACTTGGCACCTGAC

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	94.40%	5.60%	0.00%	0.00%	NA
All Indica	2759	97.50%	2.50%	0.00%	0.00%	NA
All Japonica	1512	99.90%	0.10%	0.00%	0.00%	NA
Aus	269	29.00%	71.00%	0.00%	0.00%	NA
Indica I	595	99.80%	0.20%	0.00%	0.00%	NA
Indica II	465	90.30%	9.70%	0.00%	0.00%	NA
Indica III	913	99.30%	0.70%	0.00%	0.00%	NA
Indica Intermediate	786	97.70%	2.30%	0.00%	0.00%	NA
Temperate Japonica	767	100.00%	0.00%	0.00%	0.00%	NA
Tropical Japonica	504	100.00%	0.00%	0.00%	0.00%	NA
Japonica Intermediate	241	99.60%	0.40%	0.00%	0.00%	NA
VI/Aromatic	96	99.00%	1.00%	0.00%	0.00%	NA
Intermediate	90	97.80%	2.20%	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
vg0914999957	C -> T	LOC_Os09g25080.1	upstream_gene_variant ; 4036.0bp to feature; MODIFIER	silent_mutation	Average:33.925; most accessible tissue: Minghui63 young leaf, score: 49.581	N	N	N	N
vg0914999957	C -> T	LOC_Os09g25070-LOC_Os09g25080	intergenic_region ; MODIFIER	silent_mutation	Average:33.925; most accessible tissue: Minghui63 young leaf, score: 49.581	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0914999957	5.62E-07	5.62E-07	mr1335_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