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Detailed information for vg0804312174:

Variant ID: vg0804312174 (JBrowse)	Variation Type: SNP
Chromosome: chr08	Position: 4312174
Reference Allele: T	Alternative Allele: C
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.01, others allele: 0.00, population size: 304. )

Flanking Sequence (100 bp) in Reference Genome:

ATACCCTGCTTTGACACCTAAAGAGGACCTTTGAGAAGTCAGAGCTACCGTATCGAGCTAGCGTTCAACGAGCTGTTGGCAACAATGACTAGAAGGGTTC[T/C]
GCTTAGTTTCAAGCAGGGTTTGGTTGTTGTCTTCTAAGTCAGAGCTGCAGCACTTTTGCGAGCTCGCCAACGATGACCGAAGTCTACAAGGCTCATCAGT

Reverse complement sequence

ACTGATGAGCCTTGTAGACTTCGGTCATCGTTGGCGAGCTCGCAAAAGTGCTGCAGCTCTGACTTAGAAGACAACAACCAAACCCTGCTTGAAACTAAGC[A/G]
GAACCCTTCTAGTCATTGTTGCCAACAGCTCGTTGAACGCTAGCTCGATACGGTAGCTCTGACTTCTCAAAGGTCCTCTTTAGGTGTCAAAGCAGGGTAT

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	81.10%	18.70%	0.08%	0.04%	NA
All Indica	2759	95.90%	4.00%	0.14%	0.00%	NA
All Japonica	1512	50.30%	49.60%	0.00%	0.07%	NA
Aus	269	99.30%	0.70%	0.00%	0.00%	NA
Indica I	595	93.90%	5.70%	0.34%	0.00%	NA
Indica II	465	88.80%	11.00%	0.22%	0.00%	NA
Indica III	913	99.80%	0.20%	0.00%	0.00%	NA
Indica Intermediate	786	97.10%	2.80%	0.13%	0.00%	NA
Temperate Japonica	767	45.10%	54.90%	0.00%	0.00%	NA
Tropical Japonica	504	44.00%	55.80%	0.00%	0.20%	NA
Japonica Intermediate	241	80.10%	19.90%	0.00%	0.00%	NA
VI/Aromatic	96	90.60%	9.40%	0.00%	0.00%	NA
Intermediate	90	82.20%	16.70%	0.00%	1.11%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0804312174	T -> C	LOC_Os08g07710.1	downstream_gene_variant ; 103.0bp to feature; MODIFIER	silent_mutation	Average:65.958; most accessible tissue: Zhenshan97 panicle, score: 77.482	N	N	N	N
vg0804312174	T -> C	LOC_Os08g07720.1	downstream_gene_variant ; 3986.0bp to feature; MODIFIER	silent_mutation	Average:65.958; most accessible tissue: Zhenshan97 panicle, score: 77.482	N	N	N	N
vg0804312174	T -> C	LOC_Os08g07710-LOC_Os08g07720	intergenic_region ; MODIFIER	silent_mutation	Average:65.958; most accessible tissue: Zhenshan97 panicle, score: 77.482	N	N	N	N
vg0804312174	T -> DEL	N	N	silent_mutation	Average:65.958; most accessible tissue: Zhenshan97 panicle, score: 77.482	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0804312174	2.47E-07	NA	mr1036	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
vg0804312174	NA	5.01E-06	mr1044	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
vg0804312174	5.57E-07	NA	mr1083	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
vg0804312174	8.96E-18	NA	mr1174	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
vg0804312174	2.04E-14	3.74E-17	mr1174	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
vg0804312174	6.02E-06	NA	mr1204	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
vg0804312174	NA	1.17E-07	mr1317	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
vg0804312174	9.85E-12	2.81E-07	mr1347	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
vg0804312174	4.84E-09	4.84E-09	mr1347	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
vg0804312174	NA	1.92E-06	mr1408	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
vg0804312174	NA	9.28E-07	mr1498	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
vg0804312174	NA	1.54E-06	mr1510	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
vg0804312174	NA	3.91E-08	mr1804	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
vg0804312174	NA	7.58E-08	mr1915	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
vg0804312174	1.21E-14	NA	mr1174_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
vg0804312174	1.29E-11	2.49E-12	mr1174_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
vg0804312174	2.28E-07	NA	mr1347_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
vg0804312174	3.62E-07	NA	mr1347_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