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Detailed information for vg1009413787:

Variant ID: vg1009413787 (JBrowse)	Variation Type: SNP
Chromosome: chr10	Position: 9413787
Reference Allele: A	Alternative Allele: G
Primary Allele: A	Secondary Allele: G

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.96, G: 0.04, others allele: 0.00, population size: 81. )

Flanking Sequence (100 bp) in Reference Genome:

AGCCTAAACGGTATTCCTTTCTGTGGAGGAATCAAAACAGGAGGAGAGCTGAGATACTCCTTGATATTATCCAAAGCCTTTTGCTGCTCTGCCCCCCCCC[A/G]
AGTAAATTGCTGATCGGCTTTTAATCTAAATAAGGGTGTAAAAGGTTCCAACCTTCTGGACAAATTAGAAATAAACCTTTTAACAAAATTTATCTTGCCG

Reverse complement sequence

CGGCAAGATAAATTTTGTTAAAAGGTTTATTTCTAATTTGTCCAGAAGGTTGGAACCTTTTACACCCTTATTTAGATTAAAAGCCGATCAGCAATTTACT[T/C]
GGGGGGGGGCAGAGCAGCAAAAGGCTTTGGATAATATCAAGGAGTATCTCAGCTCTCCTCCTGTTTTGATTCCTCCACAGAAAGGAATACCGTTTAGGCT

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	48.40%	39.00%	9.54%	3.05%	NA
All Indica	2759	43.80%	50.60%	5.58%	0.00%	NA
All Japonica	1512	63.60%	20.40%	7.94%	8.07%	NA
Aus	269	6.30%	34.90%	53.16%	5.58%	NA
Indica I	595	29.90%	60.30%	9.75%	0.00%	NA
Indica II	465	61.90%	35.10%	3.01%	0.00%	NA
Indica III	913	40.50%	56.80%	2.63%	0.00%	NA
Indica Intermediate	786	47.50%	45.20%	7.38%	0.00%	NA
Temperate Japonica	767	73.10%	5.10%	11.34%	10.43%	NA
Tropical Japonica	504	56.50%	40.10%	2.58%	0.79%	NA
Japonica Intermediate	241	48.10%	27.80%	8.30%	15.77%	NA
VI/Aromatic	96	47.90%	24.00%	25.00%	3.12%	NA
Intermediate	90	58.90%	25.60%	11.11%	4.44%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1009413787	A -> G	LOC_Os10g18560.1	missense_variant ; p.Trp514Arg; MODERATE	nonsynonymous_codon ; W514R	Average:32.593; most accessible tissue: Minghui63 panicle, score: 50.413	probably damaging	2.864	DELETERIOUS	0.00
vg1009413787	A -> DEL	LOC_Os10g18560.1	N	frameshift_variant	Average:32.593; most accessible tissue: Minghui63 panicle, score: 50.413	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1009413787	NA	4.42E-06	mr1118	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
vg1009413787	NA	6.08E-07	mr1495	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
vg1009413787	NA	3.88E-07	mr1709	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
vg1009413787	NA	1.04E-08	mr1027_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
vg1009413787	3.53E-08	4.44E-09	mr1053_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
vg1009413787	NA	4.73E-06	mr1118_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
vg1009413787	3.22E-07	1.60E-07	mr1147_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
vg1009413787	NA	5.78E-12	mr1258_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
vg1009413787	NA	3.71E-06	mr1264_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
vg1009413787	NA	2.84E-09	mr1495_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
vg1009413787	2.58E-06	2.58E-06	mr1516_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
vg1009413787	NA	4.96E-08	mr1709_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
vg1009413787	NA	2.44E-09	mr1709_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
vg1009413787	4.85E-06	4.85E-06	mr1941_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