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Detailed information for vg1009415346:

Variant ID: vg1009415346 (JBrowse)	Variation Type: SNP
Chromosome: chr10	Position: 9415346
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: 0.03, others allele: 0.00, population size: 80. )

Flanking Sequence (100 bp) in Reference Genome:

TGGATTACCACCAAAGTCTTTGAGCACCATATTTGTCTTGATGAGATCCTCAGCGTTCCTACCCAGCTTCCTGAACGTAGCATAAGGCATCAAGTTCACC[G/A]
CGGCCCCACCATCGACCATCATCTTAGACAACGGCTTCCCATTTACGTAGCCGTTTATATACAATGGTTTAAGATGTCGATTCTCTGTCCCCTCGGGTTT

Reverse complement sequence

AAACCCGAGGGGACAGAGAATCGACATCTTAAACCATTGTATATAAACGGCTACGTAAATGGGAAGCCGTTGTCTAAGATGATGGTCGATGGTGGGGCCG[C/T]
GGTGAACTTGATGCCTTATGCTACGTTCAGGAAGCTGGGTAGGAACGCTGAGGATCTCATCAAGACAAATATGGTGCTCAAAGACTTTGGTGGTAATCCA

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	37.00%	0.50%	20.91%	41.56%	NA
All Indica	2759	38.10%	0.70%	24.07%	37.11%	NA
All Japonica	1512	39.80%	0.10%	3.17%	56.94%	NA
Aus	269	5.60%	1.50%	87.36%	5.58%	NA
Indica I	595	25.50%	1.00%	16.97%	56.47%	NA
Indica II	465	56.30%	0.90%	16.13%	26.67%	NA
Indica III	913	33.80%	0.20%	33.95%	31.98%	NA
Indica Intermediate	786	41.90%	0.90%	22.65%	34.61%	NA
Temperate Japonica	767	55.70%	0.00%	0.91%	43.42%	NA
Tropical Japonica	504	17.30%	0.20%	5.56%	76.98%	NA
Japonica Intermediate	241	36.50%	0.00%	5.39%	58.09%	NA
VI/Aromatic	96	42.70%	1.00%	20.83%	35.42%	NA
Intermediate	90	43.30%	0.00%	23.33%	33.33%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1009415346	G -> A	LOC_Os10g18560.1	missense_variant ; p.Ala142Val; MODERATE	nonsynonymous_codon ; A142V	Average:19.116; most accessible tissue: Minghui63 young leaf, score: 28.65	benign	0.652	TOLERATED	0.08
vg1009415346	G -> DEL	LOC_Os10g18560.1	N	frameshift_variant	Average:19.116; most accessible tissue: Minghui63 young leaf, score: 28.65	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1009415346	6.82E-06	3.08E-06	mr1053	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
vg1009415346	NA	1.33E-06	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
vg1009415346	NA	3.62E-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
vg1009415346	NA	3.10E-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
vg1009415346	3.48E-08	7.32E-09	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
vg1009415346	2.81E-06	NA	mr1070_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
vg1009415346	5.93E-06	NA	mr1076_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
vg1009415346	NA	1.15E-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
vg1009415346	5.21E-06	9.75E-06	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
vg1009415346	6.01E-06	NA	mr1145_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
vg1009415346	2.93E-08	5.24E-08	mr1147_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
vg1009415346	3.60E-06	3.60E-06	mr1250_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
vg1009415346	2.13E-06	1.67E-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
vg1009415346	NA	1.73E-10	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
vg1009415346	NA	2.31E-06	mr1936_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