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Detailed information for vg1009327905:

Variant ID: vg1009327905 (JBrowse)	Variation Type: SNP
Chromosome: chr10	Position: 9327905
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.98, A: 0.01, others allele: 0.00, population size: 232. )

Flanking Sequence (100 bp) in Reference Genome:

GGCCGCGTTCGGCACTTGCACAGAGGCGGCAGGGGCCGAAGGCGTTTGAGATGGCGCAGATGTGGAAGCAGATGGTCCTCCTCCATCTTCGGCCACTGGC[G/A]
CCGAATGCTCTGCTCCCTCCTCGGCGGCCATGTCCGGTGCGGCGTTGCTTTCCTTCCGCCTTGCAACCTTCTCCTTCACGACCTTCTTCGGTGGCATTCA

Reverse complement sequence

TGAATGCCACCGAAGAAGGTCGTGAAGGAGAAGGTTGCAAGGCGGAAGGAAAGCAACGCCGCACCGGACATGGCCGCCGAGGAGGGAGCAGAGCATTCGG[C/T]
GCCAGTGGCCGAAGATGGAGGAGGACCATCTGCTTCCACATCTGCGCCATCTCAAACGCCTTCGGCCCCTGCCGCCTCTGTGCAAGTGCCGAACGCGGCC

Allele Frequencies:

Populations	Population Size	Frequency of G(primary allele)	Frequency of A(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	76.50%	5.90%	7.17%	10.41%	NA
All Indica	2759	62.40%	8.30%	11.78%	17.54%	NA
All Japonica	1512	96.50%	3.00%	0.40%	0.07%	NA
Aus	269	98.50%	0.40%	0.37%	0.74%	NA
Indica I	595	74.60%	5.00%	9.75%	10.59%	NA
Indica II	465	43.70%	15.70%	14.19%	26.45%	NA
Indica III	913	67.40%	5.90%	9.42%	17.31%	NA
Indica Intermediate	786	58.50%	9.00%	14.63%	17.81%	NA
Temperate Japonica	767	99.70%	0.30%	0.00%	0.00%	NA
Tropical Japonica	504	90.70%	8.30%	0.79%	0.20%	NA
Japonica Intermediate	241	98.30%	0.80%	0.83%	0.00%	NA
VI/Aromatic	96	97.90%	1.00%	1.04%	0.00%	NA
Intermediate	90	82.20%	5.60%	6.67%	5.56%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1009327905	G -> A	LOC_Os10g18360.1	missense_variant ; p.Ala11Val; MODERATE	nonsynonymous_codon ; A11V	Average:55.749; most accessible tissue: Zhenshan97 flag leaf, score: 80.373	unknown	unknown	TOLERATED	0.06
vg1009327905	G -> DEL	LOC_Os10g18360.1	N	frameshift_variant	Average:55.749; most accessible tissue: Zhenshan97 flag leaf, score: 80.373	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1009327905	NA	1.46E-07	mr1053	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
vg1009327905	NA	3.00E-07	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
vg1009327905	NA	8.61E-08	mr1053_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
vg1009327905	NA	1.50E-06	mr1053_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
vg1009327905	NA	3.28E-06	mr1057_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
vg1009327905	7.82E-06	2.65E-08	mr1126_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
vg1009327905	3.06E-06	3.06E-06	mr1126_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
vg1009327905	4.30E-06	NA	mr1128_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
vg1009327905	4.92E-07	2.06E-08	mr1128_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
vg1009327905	NA	3.77E-06	mr1204_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
vg1009327905	NA	1.07E-06	mr1204_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
vg1009327905	NA	6.06E-06	mr1252_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
vg1009327905	NA	6.11E-06	mr1329_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
vg1009327905	9.50E-06	9.50E-06	mr1569_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
vg1009327905	4.68E-06	4.68E-06	mr1730_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
vg1009327905	NA	1.84E-06	mr1757_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
vg1009327905	NA	4.30E-06	mr1849_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
vg1009327905	NA	8.23E-07	mr1866_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
vg1009327905	NA	9.10E-06	mr1955_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
vg1009327905	NA	4.35E-06	mr1982_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