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Detailed information for vg0217125730:

Variant ID: vg0217125730 (JBrowse)	Variation Type: SNP
Chromosome: chr02	Position: 17125730
Reference Allele: T	Alternative Allele: C
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.99, T: 0.01, others allele: 0.00, population size: 122. )

Flanking Sequence (100 bp) in Reference Genome:

AGCACCGAGCACGGCGAAGAGTCCATCGCCACCTCGATGACGGTCGCCGAAACGCCAAGCACGGCGCCGACATCGTCGCCACCTCCAACGCGGATCCGCT[T/C]
GCCAGCAGGGCATTGGTGTTGATGCGAAAAAAACACACTGACCTGGAAGATCTGCTTAACTTCAGTGCAGGTCCAAAATCTTGCTTTTAGGTTTGTGAGC

Reverse complement sequence

GCTCACAAACCTAAAAGCAAGATTTTGGACCTGCACTGAAGTTAAGCAGATCTTCCAGGTCAGTGTGTTTTTTTCGCATCAACACCAATGCCCTGCTGGC[A/G]
AGCGGATCCGCGTTGGAGGTGGCGACGATGTCGGCGCCGTGCTTGGCGTTTCGGCGACCGTCATCGAGGTGGCGATGGACTCTTCGCCGTGCTCGGTGCT

Allele Frequencies:

Populations	Population Size	Frequency of C(primary allele)	Frequency of T(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	68.90%	30.90%	0.21%	0.00%	NA
All Indica	2759	95.50%	4.40%	0.11%	0.00%	NA
All Japonica	1512	13.60%	85.90%	0.46%	0.00%	NA
Aus	269	100.00%	0.00%	0.00%	0.00%	NA
Indica I	595	99.50%	0.30%	0.17%	0.00%	NA
Indica II	465	90.10%	9.90%	0.00%	0.00%	NA
Indica III	913	94.40%	5.50%	0.11%	0.00%	NA
Indica Intermediate	786	96.90%	2.90%	0.13%	0.00%	NA
Temperate Japonica	767	15.30%	84.20%	0.52%	0.00%	NA
Tropical Japonica	504	10.70%	89.10%	0.20%	0.00%	NA
Japonica Intermediate	241	14.50%	84.60%	0.83%	0.00%	NA
VI/Aromatic	96	91.70%	8.30%	0.00%	0.00%	NA
Intermediate	90	63.30%	36.70%	0.00%	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
vg0217125730	T -> C	LOC_Os02g28910.1	missense_variant ; p.Leu155Ser; MODERATE	nonsynonymous_codon ; L155S	Average:73.903; most accessible tissue: Minghui63 young leaf, score: 84.144	unknown	unknown	TOLERATED	0.95

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0217125730	NA	1.15E-09	mr1198	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
vg0217125730	NA	6.23E-08	mr1488	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
vg0217125730	1.09E-07	NA	mr1897	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
vg0217125730	4.30E-09	1.20E-11	mr1897	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
vg0217125730	7.32E-06	7.32E-06	mr1914	Jap_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
vg0217125730	8.71E-06	NA	mr1927	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
vg0217125730	1.40E-06	1.40E-06	mr1927	Jap_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
vg0217125730	NA	6.01E-07	mr1020_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
vg0217125730	1.29E-10	NA	mr1317_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
vg0217125730	5.40E-06	5.40E-06	mr1317_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
vg0217125730	NA	1.76E-07	mr1355_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
vg0217125730	NA	5.30E-16	mr1416_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
vg0217125730	NA	8.21E-07	mr1462_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
vg0217125730	NA	3.57E-08	mr1765_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
vg0217125730	8.25E-11	6.37E-13	mr1897_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
vg0217125730	1.66E-07	1.66E-07	mr1897_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
vg0217125730	4.34E-10	NA	mr1914_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
vg0217125730	2.37E-06	2.37E-06	mr1914_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