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Detailed information for vg1111154872:

Variant ID: vg1111154872 (JBrowse)	Variation Type: SNP
Chromosome: chr11	Position: 11154872
Reference Allele: T	Alternative Allele: C
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, T: 0.01, others allele: 0.00, population size: 113. )

Flanking Sequence (100 bp) in Reference Genome:

TCAGGGCGACCAATAACACTGCAGAATACGAAGGACTACTCGCAGGGATACGAGCTGCAGCCGCACTTGGGGCCAAGCGACTAATCGTCAAAGGGGACTC[T/C]
GAGCTAGTCGCGAACCAGGTGCACAAAGACTATAAATGCTCTAACCCCGAGTTATCCAAGTATCTCGCAGAAGTCAGGAAGCTAGAGAAGAGGTTCGATG

Reverse complement sequence

CATCGAACCTCTTCTCTAGCTTCCTGACTTCTGCGAGATACTTGGATAACTCGGGGTTAGAGCATTTATAGTCTTTGTGCACCTGGTTCGCGACTAGCTC[A/G]
GAGTCCCCTTTGACGATTAGTCGCTTGGCCCCAAGTGCGGCTGCAGCTCGTATCCCTGCGAGTAGTCCTTCGTATTCTGCAGTGTTATTGGTCGCCCTGA

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	62.90%	34.60%	2.48%	0.00%	NA
All Indica	2759	93.60%	2.80%	3.59%	0.00%	NA
All Japonica	1512	5.20%	94.70%	0.07%	0.00%	NA
Aus	269	90.00%	4.10%	5.95%	0.00%	NA
Indica I	595	95.30%	4.00%	0.67%	0.00%	NA
Indica II	465	98.70%	0.60%	0.65%	0.00%	NA
Indica III	913	88.80%	2.20%	8.98%	0.00%	NA
Indica Intermediate	786	94.80%	3.90%	1.27%	0.00%	NA
Temperate Japonica	767	3.90%	96.10%	0.00%	0.00%	NA
Tropical Japonica	504	8.50%	91.30%	0.20%	0.00%	NA
Japonica Intermediate	241	2.50%	97.50%	0.00%	0.00%	NA
VI/Aromatic	96	14.60%	85.40%	0.00%	0.00%	NA
Intermediate	90	61.10%	37.80%	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
vg1111154872	T -> C	LOC_Os11g19390.1	synonymous_variant ; p.Ser67Ser; LOW	synonymous_codon	Average:32.988; most accessible tissue: Zhenshan97 panicle, score: 49.416	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1111154872	1.44E-06	NA	mr1150_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
vg1111154872	NA	9.67E-07	mr1275_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
vg1111154872	NA	1.02E-07	mr1659_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
vg1111154872	5.38E-06	NA	mr1850_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