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Detailed information for vg1002107770:

Variant ID: vg1002107770 (JBrowse)	Variation Type: SNP
Chromosome: chr10	Position: 2107770
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.00, others allele: 0.00, population size: 286. )

Flanking Sequence (100 bp) in Reference Genome:

CATATAGAACACTTATTTTGCTCTACAATTTTTGTGTATTATTTTTCCCTCAGTTAGAAAGCAATGCCGAACTTCCATCAACCAAATTAACTACTAGATC[G/A]
GCGCTTTCTCATAGTTTTGAATCCATTCTTGTCATCGACAAAAGATGTACCAGATGATACATACTTAGTATAAGGTGGTATTCGTGATTTCCATGTTACT

Reverse complement sequence

AGTAACATGGAAATCACGAATACCACCTTATACTAAGTATGTATCATCTGGTACATCTTTTGTCGATGACAAGAATGGATTCAAAACTATGAGAAAGCGC[C/T]
GATCTAGTAGTTAATTTGGTTGATGGAAGTTCGGCATTGCTTTCTAACTGAGGGAAAAATAATACACAAAAATTGTAGAGCAAAATAAGTGTTCTATATG

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	91.50%	8.10%	0.36%	0.00%	NA
All Indica	2759	89.70%	10.20%	0.11%	0.00%	NA
All Japonica	1512	92.70%	6.50%	0.86%	0.00%	NA
Aus	269	100.00%	0.00%	0.00%	0.00%	NA
Indica I	595	73.90%	26.10%	0.00%	0.00%	NA
Indica II	465	98.90%	1.10%	0.00%	0.00%	NA
Indica III	913	91.50%	8.20%	0.33%	0.00%	NA
Indica Intermediate	786	94.00%	6.00%	0.00%	0.00%	NA
Temperate Japonica	767	99.00%	0.50%	0.52%	0.00%	NA
Tropical Japonica	504	93.50%	6.00%	0.60%	0.00%	NA
Japonica Intermediate	241	71.00%	26.60%	2.49%	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
vg1002107770	G -> A	LOC_Os10g04470.1	stop_gained ; p.Arg463*; HIGH	stop_gained	Average:30.939; most accessible tissue: Zhenshan97 young leaf, score: 58.398	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1002107770	1.90E-08	NA	mr1486	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
vg1002107770	2.59E-09	6.34E-06	mr1486	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
vg1002107770	4.08E-09	NA	mr1548	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
vg1002107770	3.88E-08	9.29E-06	mr1548	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
vg1002107770	9.43E-08	NA	mr1588	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
vg1002107770	3.11E-07	1.20E-06	mr1588	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
vg1002107770	NA	5.62E-08	mr1709	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
vg1002107770	3.56E-08	NA	mr1486_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
vg1002107770	9.66E-10	NA	mr1486_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
vg1002107770	2.46E-08	NA	mr1588_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
vg1002107770	1.63E-09	9.98E-07	mr1588_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
vg1002107770	4.67E-07	8.77E-15	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
vg1002107770	NA	1.90E-10	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