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Detailed information for vg0617876285:

Variant ID: vg0617876285 (JBrowse)	Variation Type: SNP
Chromosome: chr06	Position: 17876285
Reference Allele: A	Alternative Allele: G
Primary Allele: A	Secondary Allele: G

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 1.01, others allele: 0.00, population size: 236. )

Flanking Sequence (100 bp) in Reference Genome:

TAAATCATCAGTATCTACAACTTTTGTTTTGGTCATTTTGGTATATTACTCTGTTTCAATAATTTGAATTTGAATTTCAAATTATGACAACCTGCAAACA[A/G]
CATTTTCAACCGAACTTTTATTTTAGTCATTTCTTCAACCGATAAAGTGATAGTAACATTGTTCACAAAATTTACATTTCTCTTATATGGTTTTGAAGTA

Reverse complement sequence

TACTTCAAAACCATATAAGAGAAATGTAAATTTTGTGAACAATGTTACTATCACTTTATCGGTTGAAGAAATGACTAAAATAAAAGTTCGGTTGAAAATG[T/C]
TGTTTGCAGGTTGTCATAATTTGAAATTCAAATTCAAATTATTGAAACAGAGTAATATACCAAAATGACCAAAACAAAAGTTGTAGATACTGATGATTTA

Allele Frequencies:

Populations	Population Size	Frequency of A(primary allele)	Frequency of G(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	90.70%	7.40%	1.90%	0.00%	NA
All Indica	2759	84.50%	12.40%	3.19%	0.00%	NA
All Japonica	1512	99.70%	0.30%	0.07%	0.00%	NA
Aus	269	99.60%	0.40%	0.00%	0.00%	NA
Indica I	595	89.90%	3.00%	7.06%	0.00%	NA
Indica II	465	92.70%	3.00%	4.30%	0.00%	NA
Indica III	913	75.00%	24.30%	0.66%	0.00%	NA
Indica Intermediate	786	86.40%	11.10%	2.54%	0.00%	NA
Temperate Japonica	767	99.30%	0.50%	0.13%	0.00%	NA
Tropical Japonica	504	100.00%	0.00%	0.00%	0.00%	NA
Japonica Intermediate	241	100.00%	0.00%	0.00%	0.00%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	93.30%	5.60%	1.11%	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
vg0617876285	A -> G	LOC_Os06g30820.1	upstream_gene_variant ; 2019.0bp to feature; MODIFIER	silent_mutation	Average:49.744; most accessible tissue: Zhenshan97 panicle, score: 75.67	N	N	N	N
vg0617876285	A -> G	LOC_Os06g30820.4	upstream_gene_variant ; 2019.0bp to feature; MODIFIER	silent_mutation	Average:49.744; most accessible tissue: Zhenshan97 panicle, score: 75.67	N	N	N	N
vg0617876285	A -> G	LOC_Os06g30820.3	upstream_gene_variant ; 2028.0bp to feature; MODIFIER	silent_mutation	Average:49.744; most accessible tissue: Zhenshan97 panicle, score: 75.67	N	N	N	N
vg0617876285	A -> G	LOC_Os06g30820.2	upstream_gene_variant ; 2028.0bp to feature; MODIFIER	silent_mutation	Average:49.744; most accessible tissue: Zhenshan97 panicle, score: 75.67	N	N	N	N
vg0617876285	A -> G	LOC_Os06g30820-LOC_Os06g30830	intergenic_region ; MODIFIER	silent_mutation	Average:49.744; most accessible tissue: Zhenshan97 panicle, score: 75.67	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0617876285	1.52E-07	NA	mr1065_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
vg0617876285	4.70E-06	NA	mr1067_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
vg0617876285	1.86E-08	1.81E-08	mr1068_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
vg0617876285	4.44E-08	6.98E-08	mr1078_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
vg0617876285	6.18E-10	1.84E-10	mr1087_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
vg0617876285	5.12E-09	9.11E-09	mr1090_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
vg0617876285	3.14E-06	NA	mr1091_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
vg0617876285	1.15E-06	2.54E-07	mr1094_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
vg0617876285	2.37E-06	2.43E-07	mr1096_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
vg0617876285	8.73E-07	NA	mr1108_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
vg0617876285	2.23E-07	6.68E-07	mr1110_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
vg0617876285	1.27E-09	1.02E-08	mr1111_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
vg0617876285	5.02E-07	NA	mr1112_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
vg0617876285	1.92E-08	4.33E-08	mr1121_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
vg0617876285	1.64E-09	2.25E-09	mr1144_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
vg0617876285	1.68E-06	NA	mr1200_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
vg0617876285	1.38E-06	1.15E-06	mr1211_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
vg0617876285	3.25E-08	NA	mr1234_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
vg0617876285	3.08E-07	6.10E-08	mr1526_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