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Detailed information for vg1125545839:

Variant ID: vg1125545839 (JBrowse)	Variation Type: SNP
Chromosome: chr11	Position: 25545839
Reference Allele: T	Alternative Allele: C
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.82, C: 0.18, others allele: 0.00, population size: 115. )

Flanking Sequence (100 bp) in Reference Genome:

TGATCATTCATGGCGGCGTGCGTGTCCGCGTGATCCACCGCGTGTCATCGTCTCTGCAGGCCAGGCCGTTCCTGTACGGAGGAGGCGGTGATGGCGACGA[T/C]
GATGACGACGACGCGGTGAGGATGATGGTGGATCCTGCTCTCGGCGGCCAGTACGACGCCGGGCAGCTCGCCGTCGTCGCCTACGCCGCCAAGATCTGCA

Reverse complement sequence

TGCAGATCTTGGCGGCGTAGGCGACGACGGCGAGCTGCCCGGCGTCGTACTGGCCGCCGAGAGCAGGATCCACCATCATCCTCACCGCGTCGTCGTCATC[A/G]
TCGTCGCCATCACCGCCTCCTCCGTACAGGAACGGCCTGGCCTGCAGAGACGATGACACGCGGTGGATCACGCGGACACGCACGCCGCCATGAATGATCA

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	87.50%	12.40%	0.11%	0.00%	NA
All Indica	2759	85.30%	14.60%	0.11%	0.00%	NA
All Japonica	1512	98.10%	1.90%	0.00%	0.00%	NA
Aus	269	67.70%	32.00%	0.37%	0.00%	NA
Indica I	595	67.40%	32.40%	0.17%	0.00%	NA
Indica II	465	80.90%	19.10%	0.00%	0.00%	NA
Indica III	913	95.10%	4.90%	0.00%	0.00%	NA
Indica Intermediate	786	90.20%	9.50%	0.25%	0.00%	NA
Temperate Japonica	767	97.50%	2.50%	0.00%	0.00%	NA
Tropical Japonica	504	99.60%	0.40%	0.00%	0.00%	NA
Japonica Intermediate	241	97.10%	2.90%	0.00%	0.00%	NA
VI/Aromatic	96	44.80%	55.20%	0.00%	0.00%	NA
Intermediate	90	78.90%	20.00%	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
vg1125545839	T -> C	LOC_Os11g42440.1	synonymous_variant ; p.Asp479Asp; LOW	synonymous_codon	Average:66.941; most accessible tissue: Minghui63 panicle, score: 85.556	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1125545839	1.81E-37	1.15E-47	mr1191	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
vg1125545839	2.51E-21	3.55E-25	mr1191	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
vg1125545839	NA	3.07E-06	mr1530	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
vg1125545839	3.08E-41	1.34E-56	mr1644	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
vg1125545839	3.69E-23	5.05E-28	mr1644	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
vg1125545839	3.53E-10	4.04E-18	mr1662	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
vg1125545839	8.78E-08	1.65E-11	mr1662	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
vg1125545839	NA	1.99E-06	mr1745	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
vg1125545839	6.95E-59	2.51E-75	mr1191_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
vg1125545839	2.28E-33	3.29E-44	mr1191_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
vg1125545839	NA	4.37E-08	mr1522_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
vg1125545839	NA	2.80E-07	mr1530_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
vg1125545839	6.30E-13	3.25E-26	mr1662_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
vg1125545839	2.22E-07	3.49E-13	mr1662_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
vg1125545839	NA	2.46E-10	mr1745_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