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Detailed information for vg0802266533:

Variant ID: vg0802266533 (JBrowse)	Variation Type: SNP
Chromosome: chr08	Position: 2266533
Reference Allele: T	Alternative Allele: C
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

AAGGGGAGCATGAAGAGGAGCGCATCGTGGCCGAGCGAGAAGGCCATGCCGCCGGTGACCCGTCACTCTGGCGGGCACTCAACCTGCTCCACAACCACCT[T/C]
GCGCACTTAATGTCGTGGGACGCGCTGACGGAGGCACTCGCGCGTCTCCACGACGACGTCCGCCGCCGCACCTGCACGACATTTGTGCCATCTGCACGTC

Reverse complement sequence

GACGTGCAGATGGCACAAATGTCGTGCAGGTGCGGCGGCGGACGTCGTCGTGGAGACGCGCGAGTGCCTCCGTCAGCGCGTCCCACGACATTAAGTGCGC[A/G]
AGGTGGTTGTGGAGCAGGTTGAGTGCCCGCCAGAGTGACGGGTCACCGGCGGCATGGCCTTCTCGCTCGGCCACGATGCGCTCCTCTTCATGCTCCCCTT

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	89.20%	7.90%	2.43%	0.42%	NA
All Indica	2759	99.20%	0.10%	0.04%	0.69%	NA
All Japonica	1512	68.30%	24.40%	7.28%	0.00%	NA
Aus	269	100.00%	0.00%	0.00%	0.00%	NA
Indica I	595	99.80%	0.00%	0.17%	0.00%	NA
Indica II	465	99.60%	0.20%	0.00%	0.22%	NA
Indica III	913	99.00%	0.00%	0.00%	0.99%	NA
Indica Intermediate	786	98.70%	0.10%	0.00%	1.15%	NA
Temperate Japonica	767	47.80%	41.20%	10.95%	0.00%	NA
Tropical Japonica	504	97.20%	1.40%	1.39%	0.00%	NA
Japonica Intermediate	241	73.00%	19.10%	7.88%	0.00%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	90.00%	4.40%	4.44%	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
vg0802266533	T -> C	LOC_Os08g04550.1	synonymous_variant ; p.Leu181Leu; LOW	synonymous_codon	Average:73.819; most accessible tissue: Zhenshan97 young leaf, score: 86.055	N	N	N	N
vg0802266533	T -> DEL	LOC_Os08g04550.1	N	frameshift_variant	Average:73.819; most accessible tissue: Zhenshan97 young leaf, score: 86.055	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0802266533	NA	6.93E-08	mr1977_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