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Detailed information for vg0324095631:

Variant ID: vg0324095631 (JBrowse)	Variation Type: SNP
Chromosome: chr03	Position: 24095631
Reference Allele: T	Alternative Allele: C
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 1.00, others allele: 0.00, population size: 36. )

Flanking Sequence (100 bp) in Reference Genome:

GGAAGAACACTTTCAAATCTTGGCCATCTCTTGAGAAAACTTCACCCGAGAAAAGCTGGGTTACATGGTACAAGCGCGTATCGGCTAGTAAGCAAACACA[T/C]
TGGGACGAGATTGGAATCGGCCAAGCACTTGCCCTCACCATAGCAAATTCGGCTAAGGACGAACCCTTAATAGCCGCTGCCACCTATTTCTGGTCCAATA

Reverse complement sequence

TATTGGACCAGAAATAGGTGGCAGCGGCTATTAAGGGTTCGTCCTTAGCCGAATTTGCTATGGTGAGGGCAAGTGCTTGGCCGATTCCAATCTCGTCCCA[A/G]
TGTGTTTGCTTACTAGCCGATACGCGCTTGTACCATGTAACCCAGCTTTTCTCGGGTGAAGTTTTCTCAAGAGATGGCCAAGATTTGAAAGTGTTCTTCC

Allele Frequencies:

Populations	Population Size	Frequency of T(primary allele)	Frequency of C(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	41.50%	3.40%	2.26%	52.79%	NA
All Indica	2759	5.10%	5.50%	2.28%	87.17%	NA
All Japonica	1512	99.10%	0.10%	0.07%	0.73%	NA
Aus	269	75.50%	1.90%	9.67%	13.01%	NA
Indica I	595	6.70%	3.40%	2.86%	87.06%	NA
Indica II	465	3.20%	7.50%	1.72%	87.53%	NA
Indica III	913	1.60%	5.60%	2.52%	90.25%	NA
Indica Intermediate	786	8.90%	5.70%	1.91%	83.46%	NA
Temperate Japonica	767	99.50%	0.00%	0.00%	0.52%	NA
Tropical Japonica	504	98.80%	0.40%	0.20%	0.60%	NA
Japonica Intermediate	241	98.30%	0.00%	0.00%	1.66%	NA
VI/Aromatic	96	76.00%	1.00%	16.67%	6.25%	NA
Intermediate	90	53.30%	3.30%	1.11%	42.22%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0324095631	T -> C	LOC_Os03g43210.1	synonymous_variant ; p.His100His; LOW	synonymous_codon	Average:23.847; most accessible tissue: Minghui63 young leaf, score: 61.887	N	N	N	N
vg0324095631	T -> DEL	LOC_Os03g43210.1	N	frameshift_variant	Average:23.847; most accessible tissue: Minghui63 young leaf, score: 61.887	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0324095631	NA	4.15E-15	mr1164	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
vg0324095631	NA	1.04E-07	mr1220	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
vg0324095631	NA	5.94E-23	mr1571	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
vg0324095631	NA	8.19E-12	mr1940	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
vg0324095631	3.29E-07	3.29E-07	mr1987	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
vg0324095631	NA	2.40E-08	mr1084_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
vg0324095631	NA	3.30E-16	mr1133_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
vg0324095631	NA	2.72E-09	mr1198_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
vg0324095631	NA	3.96E-07	mr1205_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
vg0324095631	NA	1.25E-21	mr1401_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
vg0324095631	NA	4.99E-13	mr1521_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
vg0324095631	NA	7.10E-15	mr1575_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
vg0324095631	NA	3.81E-11	mr1667_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
vg0324095631	NA	7.37E-08	mr1681_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
vg0324095631	NA	8.52E-06	mr1869_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
vg0324095631	NA	3.41E-07	mr1885_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
vg0324095631	NA	6.92E-20	mr1922_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
vg0324095631	NA	6.86E-09	mr1940_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