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Detailed information for vg0517841440:

Variant ID: vg0517841440 (JBrowse)	Variation Type: SNP
Chromosome: chr05	Position: 17841440
Reference Allele: C	Alternative Allele: T
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.93, T: 0.07, others allele: 0.00, population size: 103. )

Flanking Sequence (100 bp) in Reference Genome:

AAATAATCCACAGCTTCTAAGAATCTGTAGTTATAGATTCTGAAAAATGAACTAAGAAGCCAGAAGCTGGAGAAGCTGGGTTTCAGAGTTTTTCCAGATT[C/T]
TCAGAAGCTGGCTACCAAACAGCTGCTTCTCAGAATCTAAAGCTCCTCCAAACAGACCCGTAGTCCATCAATTTAAGTCTTAGTAATATGCAAATTTAGG

Reverse complement sequence

CCTAAATTTGCATATTACTAAGACTTAAATTGATGGACTACGGGTCTGTTTGGAGGAGCTTTAGATTCTGAGAAGCAGCTGTTTGGTAGCCAGCTTCTGA[G/A]
AATCTGGAAAAACTCTGAAACCCAGCTTCTCCAGCTTCTGGCTTCTTAGTTCATTTTTCAGAATCTATAACTACAGATTCTTAGAAGCTGTGGATTATTT

Allele Frequencies:

Populations	Population Size	Frequency of T(primary allele)	Frequency of C(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	64.40%	35.30%	0.34%	0.00%	NA
All Indica	2759	94.10%	5.70%	0.29%	0.00%	NA
All Japonica	1512	8.30%	91.30%	0.33%	0.00%	NA
Aus	269	99.60%	0.40%	0.00%	0.00%	NA
Indica I	595	100.00%	0.00%	0.00%	0.00%	NA
Indica II	465	74.60%	24.70%	0.65%	0.00%	NA
Indica III	913	99.00%	0.80%	0.22%	0.00%	NA
Indica Intermediate	786	95.30%	4.30%	0.38%	0.00%	NA
Temperate Japonica	767	3.30%	96.70%	0.00%	0.00%	NA
Tropical Japonica	504	18.50%	81.00%	0.60%	0.00%	NA
Japonica Intermediate	241	3.30%	95.90%	0.83%	0.00%	NA
VI/Aromatic	96	7.30%	91.70%	1.04%	0.00%	NA
Intermediate	90	52.20%	45.60%	2.22%	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
vg0517841440	C -> T	LOC_Os05g30770.1	upstream_gene_variant ; 4382.0bp to feature; MODIFIER	silent_mutation	Average:45.19; most accessible tissue: Minghui63 panicle, score: 77.956	N	N	N	N
vg0517841440	C -> T	LOC_Os05g30780.1	downstream_gene_variant ; 706.0bp to feature; MODIFIER	silent_mutation	Average:45.19; most accessible tissue: Minghui63 panicle, score: 77.956	N	N	N	N
vg0517841440	C -> T	LOC_Os05g30770-LOC_Os05g30780	intergenic_region ; MODIFIER	silent_mutation	Average:45.19; most accessible tissue: Minghui63 panicle, score: 77.956	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0517841440	5.40E-07	NA	mr1155_2	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
vg0517841440	NA	2.03E-07	mr1408_2	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
vg0517841440	NA	1.11E-07	mr1654_2	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
vg0517841440	NA	4.29E-08	mr1783_2	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
vg0517841440	NA	1.15E-14	mr1790_2	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
vg0517841440	NA	9.54E-06	mr1806_2	Ind_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
vg0517841440	NA	2.86E-07	mr1821_2	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
vg0517841440	NA	2.32E-07	mr1837_2	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