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Detailed information for vg1123041283:

Variant ID: vg1123041283 (JBrowse)	Variation Type: SNP
Chromosome: chr11	Position: 23041283
Reference Allele: C	Alternative Allele: A
Primary Allele: C	Secondary Allele: A

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.98, A: 0.03, others allele: 0.00, population size: 195. )

Flanking Sequence (100 bp) in Reference Genome:

ATAGAAATTATTTGCCTCTATCCAGCTTTTGCGGCAGCTTTGTATTTCCTAATTTTGATTCGGTGGACCTAAAGGGATTTAGTGCTCAATATTTTTTTTT[C/A]
TTTTGAAATTGACGACGGCAGGAGCTCTGCCGGATATATTGAGAAGTAAAAGTTCAGAAGTACAAAAGGTTCTGGGAAAAGGGAGAATAGAGGAGGTTAC

Reverse complement sequence

GTAACCTCCTCTATTCTCCCTTTTCCCAGAACCTTTTGTACTTCTGAACTTTTACTTCTCAATATATCCGGCAGAGCTCCTGCCGTCGTCAATTTCAAAA[G/T]
AAAAAAAAATATTGAGCACTAAATCCCTTTAGGTCCACCGAATCAAAATTAGGAAATACAAAGCTGCCGCAAAAGCTGGATAGAGGCAAATAATTTCTAT

Allele Frequencies:

Populations	Population Size	Frequency of C(primary allele)	Frequency of A(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	74.00%	24.10%	0.04%	1.86%	NA
All Indica	2759	63.70%	35.90%	0.04%	0.36%	NA
All Japonica	1512	93.80%	5.50%	0.00%	0.66%	NA
Aus	269	68.00%	9.30%	0.37%	22.30%	NA
Indica I	595	66.70%	33.10%	0.00%	0.17%	NA
Indica II	465	64.10%	35.90%	0.00%	0.00%	NA
Indica III	913	70.40%	28.70%	0.00%	0.88%	NA
Indica Intermediate	786	53.30%	46.40%	0.13%	0.13%	NA
Temperate Japonica	767	96.20%	2.90%	0.00%	0.91%	NA
Tropical Japonica	504	95.80%	4.00%	0.00%	0.20%	NA
Japonica Intermediate	241	82.20%	17.00%	0.00%	0.83%	NA
VI/Aromatic	96	79.20%	15.60%	0.00%	5.21%	NA
Intermediate	90	70.00%	26.70%	0.00%	3.33%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1123041283	C -> A	LOC_Os11g38760-LOC_Os11g38765	intergenic_region ; MODIFIER	silent_mutation	Average:34.237; most accessible tissue: Callus, score: 58.006	N	N	N	N
vg1123041283	C -> DEL	N	N	silent_mutation	Average:34.237; most accessible tissue: Callus, score: 58.006	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1123041283	NA	3.71E-06	mr1157	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
vg1123041283	1.84E-06	1.15E-07	mr1446	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