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Detailed information for vg0907887620:

Variant ID: vg0907887620 (JBrowse)	Variation Type: SNP
Chromosome: chr09	Position: 7887620
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.65, T: 0.35, others allele: 0.00, population size: 92. )

Flanking Sequence (100 bp) in Reference Genome:

CTGTATTTTGAAACTTAATTATTATTTTTTAGAAAAGGCTATATGTACTAACTTTTTCTTACTAAATTCTTACTAACACTGATGTGTCATGCTATGAGTG[C/T]
ATCTAGATTTTTTGTAACTTCCATCTACTTAAATTAAACGGTTGAGATGATTGTTAGTAAAAGTTTAGTAAGAAAAATTTAGTACATGTAGCATTGCTCT

Reverse complement sequence

AGAGCAATGCTACATGTACTAAATTTTTCTTACTAAACTTTTACTAACAATCATCTCAACCGTTTAATTTAAGTAGATGGAAGTTACAAAAAATCTAGAT[G/A]
CACTCATAGCATGACACATCAGTGTTAGTAAGAATTTAGTAAGAAAAAGTTAGTACATATAGCCTTTTCTAAAAAATAATAATTAAGTTTCAAAATACAG

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	85.80%	14.10%	0.08%	0.00%	NA
All Indica	2759	92.90%	7.00%	0.14%	0.00%	NA
All Japonica	1512	70.60%	29.40%	0.00%	0.00%	NA
Aus	269	91.40%	8.60%	0.00%	0.00%	NA
Indica I	595	96.50%	3.50%	0.00%	0.00%	NA
Indica II	465	89.70%	10.10%	0.22%	0.00%	NA
Indica III	913	95.60%	4.20%	0.22%	0.00%	NA
Indica Intermediate	786	88.90%	10.90%	0.13%	0.00%	NA
Temperate Japonica	767	76.80%	23.20%	0.00%	0.00%	NA
Tropical Japonica	504	76.80%	23.20%	0.00%	0.00%	NA
Japonica Intermediate	241	38.20%	61.80%	0.00%	0.00%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	91.10%	8.90%	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
vg0907887620	C -> T	LOC_Os09g13590.1	downstream_gene_variant ; 506.0bp to feature; MODIFIER	silent_mutation	Average:41.304; most accessible tissue: Minghui63 panicle, score: 73.225	N	N	N	N
vg0907887620	C -> T	LOC_Os09g13570-LOC_Os09g13590	intergenic_region ; MODIFIER	silent_mutation	Average:41.304; most accessible tissue: Minghui63 panicle, score: 73.225	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0907887620	NA	9.26E-06	mr1114_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
vg0907887620	NA	7.21E-06	mr1117_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
vg0907887620	NA	5.97E-06	mr1240_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
vg0907887620	NA	6.39E-06	mr1496_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
vg0907887620	NA	1.62E-06	mr1861_2	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
vg0907887620	NA	3.84E-06	mr1977_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