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Detailed information for vg0911208644:

Variant ID: vg0911208644 (JBrowse)	Variation Type: SNP
Chromosome: chr09	Position: 11208644
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: 222. )

Flanking Sequence (100 bp) in Reference Genome:

TAGCTGATATGTGAGTTTGAGAGTCGCTATGATAGGTTTTAGAAAGCCCAAAATCTGCTATTTTGGCTTTTAGATTTCGACCCAAGAGAATGTTATTTGT[C/T]
TTCACATCCCCATGAATTATTGGCAAGTTGCAACCCTTGTGTAGATAATCCAGGCCTACACATAAGAAAACCATACTAAGAAGAAGGATTACAATATAAT

Reverse complement sequence

ATTATATTGTAATCCTTCTTCTTAGTATGGTTTTCTTATGTGTAGGCCTGGATTATCTACACAAGGGTTGCAACTTGCCAATAATTCATGGGGATGTGAA[G/A]
ACAAATAACATTCTCTTGGGTCGAAATCTAAAAGCCAAAATAGCAGATTTTGGGCTTTCTAAAACCTATCATAGCGACTCTCAAACTCACATATCAGCTA

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	73.80%	6.80%	1.61%	17.84%	NA
All Indica	2759	65.00%	4.10%	1.38%	29.50%	NA
All Japonica	1512	88.00%	9.70%	1.85%	0.53%	NA
Aus	269	99.60%	0.40%	0.00%	0.00%	NA
Indica I	595	85.40%	0.00%	0.17%	14.45%	NA
Indica II	465	44.90%	3.00%	2.15%	49.89%	NA
Indica III	913	63.00%	9.00%	1.20%	26.83%	NA
Indica Intermediate	786	63.70%	2.30%	2.04%	31.93%	NA
Temperate Japonica	767	88.50%	8.30%	2.61%	0.52%	NA
Tropical Japonica	504	95.00%	4.20%	0.40%	0.40%	NA
Japonica Intermediate	241	71.40%	25.30%	2.49%	0.83%	NA
VI/Aromatic	96	35.40%	51.00%	5.21%	8.33%	NA
Intermediate	90	67.80%	12.20%	5.56%	14.44%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0911208644	C -> DEL	LOC_Os09g18260.1	N	frameshift_variant	Average:38.335; most accessible tissue: Zhenshan97 young leaf, score: 63.096	N	N	N	N
vg0911208644	C -> T	LOC_Os09g18260.1	synonymous_variant ; p.Lys676Lys; LOW	synonymous_codon	Average:38.335; most accessible tissue: Zhenshan97 young leaf, score: 63.096	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0911208644	6.50E-07	NA	mr1350_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