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Detailed information for vg1110630869:

Variant ID: vg1110630869 (JBrowse)	Variation Type: SNP
Chromosome: chr11	Position: 10630869
Reference Allele: T	Alternative Allele: A
Primary Allele: A	Secondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

GTTTTTATTTACATAATTAGTTTGTTCTATTTAAGCTTTTTGAAAATTGCTAAAATTCAAGAATAACTTTTCCTACTTCATATTATATTATTTTTAGCTA[T/A]
TGGAATTAACGGAAAATCAATTATATATTTTTATCTTTTTGACCAAAGGTCACTGCAATTTCATTTCATTAATATTATTATTATGATTATGATTCCTTTA

Reverse complement sequence

TAAAGGAATCATAATCATAATAATAATATTAATGAAATGAAATTGCAGTGACCTTTGGTCAAAAAGATAAAAATATATAATTGATTTTCCGTTAATTCCA[A/T]
TAGCTAAAAATAATATAATATGAAGTAGGAAAAGTTATTCTTGAATTTTAGCAATTTTCAAAAAGCTTAAATAGAACAAACTAATTATGTAAATAAAAAC

Allele Frequencies:

Populations	Population Size	Frequency of A(primary allele)	Frequency of T(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	89.10%	5.30%	5.04%	0.55%	NA
All Indica	2759	97.70%	0.30%	1.12%	0.91%	NA
All Japonica	1512	71.40%	15.70%	12.90%	0.00%	NA
Aus	269	99.60%	0.00%	0.37%	0.00%	NA
Indica I	595	98.00%	0.20%	1.85%	0.00%	NA
Indica II	465	95.90%	0.40%	0.86%	2.80%	NA
Indica III	913	99.70%	0.00%	0.11%	0.22%	NA
Indica Intermediate	786	96.30%	0.50%	1.91%	1.27%	NA
Temperate Japonica	767	54.00%	27.60%	18.38%	0.00%	NA
Tropical Japonica	504	92.10%	1.80%	6.15%	0.00%	NA
Japonica Intermediate	241	83.40%	7.10%	9.54%	0.00%	NA
VI/Aromatic	96	97.90%	0.00%	2.08%	0.00%	NA
Intermediate	90	83.30%	5.60%	10.00%	1.11%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1110630869	T -> A	LOC_Os11g18740-LOC_Os11g18750	intergenic_region ; MODIFIER	silent_mutation	Average:13.724; most accessible tissue: Minghui63 panicle, score: 20.733	N	N	N	N
vg1110630869	T -> DEL	N	N	silent_mutation	Average:13.724; most accessible tissue: Minghui63 panicle, score: 20.733	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1110630869	NA	1.95E-08	mr1768	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