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Detailed information for vg1123174932:

Variant ID: vg1123174932 (JBrowse)	Variation Type: SNP
Chromosome: chr11	Position: 23174932
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, others allele: 0.00, population size: 318. )

Flanking Sequence (100 bp) in Reference Genome:

AAATTTACAGTTAGTCATCATGGTACACTGACTTGCTGTTCCATTGTCTTTCCATCTTCTGTTTCTACAGGCTTCCTTTTTGGCCATCTATGAAATTGAT[C/T]
TTTATTTGCTGGCTTGTCTTGCCATACTTCAATGGTGCAGCCTTTGTGTACCAAAATTATGTGAGACCTATGTTTGTGAAGCACCAAATGGTTAACATTT

Reverse complement sequence

AAATGTTAACCATTTGGTGCTTCACAAACATAGGTCTCACATAATTTTGGTACACAAAGGCTGCACCATTGAAGTATGGCAAGACAAGCCAGCAAATAAA[G/A]
ATCAATTTCATAGATGGCCAAAAAGGAAGCCTGTAGAAACAGAAGATGGAAAGACAATGGAACAGCAAGTCAGTGTACCATGATGACTAACTGTAAATTT

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	82.30%	17.20%	0.42%	0.00%	NA
All Indica	2759	89.70%	9.90%	0.33%	0.00%	NA
All Japonica	1512	64.30%	35.10%	0.66%	0.00%	NA
Aus	269	99.30%	0.40%	0.37%	0.00%	NA
Indica I	595	61.20%	37.50%	1.34%	0.00%	NA
Indica II	465	99.80%	0.20%	0.00%	0.00%	NA
Indica III	913	98.50%	1.50%	0.00%	0.00%	NA
Indica Intermediate	786	95.30%	4.60%	0.13%	0.00%	NA
Temperate Japonica	767	87.00%	12.50%	0.52%	0.00%	NA
Tropical Japonica	504	37.90%	60.90%	1.19%	0.00%	NA
Japonica Intermediate	241	47.30%	52.70%	0.00%	0.00%	NA
VI/Aromatic	96	99.00%	1.00%	0.00%	0.00%	NA
Intermediate	90	90.00%	10.00%	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
vg1123174932	C -> T	LOC_Os11g38920.2	synonymous_variant ; p.Ile79Ile; LOW	synonymous_codon	Average:50.835; most accessible tissue: Callus, score: 82.579	N	N	N	N
vg1123174932	C -> T	LOC_Os11g38920.1	synonymous_variant ; p.Ile4Ile; LOW	synonymous_codon	Average:50.835; most accessible tissue: Callus, score: 82.579	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1123174932	NA	9.75E-09	mr1022	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
vg1123174932	NA	3.55E-14	mr1079	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
vg1123174932	NA	1.35E-06	mr1156	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
vg1123174932	NA	7.64E-11	mr1390	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
vg1123174932	NA	1.02E-11	mr1490	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
vg1123174932	NA	4.14E-06	mr1790	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
vg1123174932	NA	3.98E-06	mr1835	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
vg1123174932	NA	4.53E-15	mr1178_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
vg1123174932	NA	2.89E-13	mr1390_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