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Detailed information for vg1001245650:

Variant ID: vg1001245650 (JBrowse)	Variation Type: SNP
Chromosome: chr10	Position: 1245650
Reference Allele: A	Alternative Allele: G
Primary Allele: A	Secondary Allele: G

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.91, A: 0.11, others allele: 0.00, population size: 36. )

Flanking Sequence (100 bp) in Reference Genome:

AGGCAAGTGTCCTGAAAATTGGTTATTATCAAGCCAAAGGTCTGGTATGCCCGTGAGATTTTCGAATTCCCGAGGAAGAGAACCTGTTAATCGGTTATGA[A/G]
ACATGGTCATCAGTTGGATGTTCACCAAGTTACCGAAAGTTTTGTAGCATCGAATCACAATAACTAAGACAACCAGGGGGGGAGGGGTGAATGGTTAGTA

Reverse complement sequence

TACTAACCATTCACCCCTCCCCCCCTGGTTGTCTTAGTTATTGTGATTCGATGCTACAAAACTTTCGGTAACTTGGTGAACATCCAACTGATGACCATGT[T/C]
TCATAACCGATTAACAGGTTCTCTTCCTCGGGAATTCGAAAATCTCACGGGCATACCAGACCTTTGGCTTGATAATAACCAATTTTCAGGACACTTGCCT

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	54.30%	16.00%	5.69%	24.02%	NA
All Indica	2759	68.70%	19.10%	6.85%	5.36%	NA
All Japonica	1512	41.30%	3.80%	1.79%	53.17%	NA
Aus	269	3.30%	52.80%	15.24%	28.62%	NA
Indica I	595	98.20%	1.50%	0.34%	0.00%	NA
Indica II	465	60.40%	21.50%	15.48%	2.58%	NA
Indica III	913	54.90%	30.40%	7.01%	7.67%	NA
Indica Intermediate	786	67.40%	17.70%	6.49%	8.40%	NA
Temperate Japonica	767	72.10%	0.70%	0.52%	26.73%	NA
Tropical Japonica	504	6.00%	9.10%	3.57%	81.35%	NA
Japonica Intermediate	241	17.00%	2.50%	2.07%	78.42%	NA
VI/Aromatic	96	6.20%	11.50%	4.17%	78.12%	NA
Intermediate	90	35.60%	21.10%	8.89%	34.44%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1001245650	A -> G	LOC_Os10g02990.1	missense_variant ; p.Phe4Ser; MODERATE	nonsynonymous_codon ; F4A	Average:39.81; most accessible tissue: Minghui63 panicle, score: 64.459	unknown	unknown	TOLERATED	0.06
vg1001245650	A -> G	LOC_Os10g02990.1	missense_variant ; p.Phe4Ser; MODERATE	nonsynonymous_codon ; F4S	Average:39.81; most accessible tissue: Minghui63 panicle, score: 64.459	unknown	unknown	TOLERATED	0.11
vg1001245650	A -> DEL	LOC_Os10g02990.1	N	frameshift_variant	Average:39.81; most accessible tissue: Minghui63 panicle, score: 64.459	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1001245650	6.30E-15	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
vg1001245650	1.26E-18	1.95E-16	mr1486	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
vg1001245650	7.49E-16	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
vg1001245650	3.59E-17	9.25E-16	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
vg1001245650	1.87E-06	NA	mr1588	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
vg1001245650	7.60E-09	4.34E-07	mr1588	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
vg1001245650	2.04E-18	NA	mr1486_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
vg1001245650	6.02E-23	8.32E-21	mr1486_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
vg1001245650	1.63E-12	NA	mr1588_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
vg1001245650	8.05E-17	6.24E-10	mr1588_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