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Detailed information for vg0222538877:

Variant ID: vg0222538877 (JBrowse)	Variation Type: SNP
Chromosome: chr02	Position: 22538877
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.98, T: 0.02, others allele: 0.00, population size: 63. )

Flanking Sequence (100 bp) in Reference Genome:

GAGGCACTTTAGTGGTAGCACTATAACATCAGATCTAAGGGGTTGTTTGGTTGGCATACTCACATTACCAAAACTTGCCATACTTCATTTAGCTAACATG[C/T]
CTAACATGTGGCCAACAAAATTGAAGCTACACTTCAGCCATAGGAGAGTAAACTTGCCACACTTTTATGTGCCAATGACATGTGGGACCCACATCATGGA

Reverse complement sequence

TCCATGATGTGGGTCCCACATGTCATTGGCACATAAAAGTGTGGCAAGTTTACTCTCCTATGGCTGAAGTGTAGCTTCAATTTTGTTGGCCACATGTTAG[G/A]
CATGTTAGCTAAATGAAGTATGGCAAGTTTTGGTAATGTGAGTATGCCAACCAAACAACCCCTTAGATCTGATGTTATAGTGCTACCACTAAAGTGCCTC

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	41.90%	1.30%	3.66%	53.15%	NA
All Indica	2759	13.40%	0.90%	4.46%	81.30%	NA
All Japonica	1512	96.70%	0.00%	0.26%	3.04%	NA
Aus	269	2.20%	12.60%	14.13%	71.00%	NA
Indica I	595	25.40%	0.20%	3.87%	70.59%	NA
Indica II	465	7.70%	0.40%	2.80%	89.03%	NA
Indica III	913	5.70%	1.20%	5.04%	88.06%	NA
Indica Intermediate	786	16.50%	1.30%	5.22%	76.97%	NA
Temperate Japonica	767	99.30%	0.00%	0.00%	0.65%	NA
Tropical Japonica	504	91.90%	0.00%	0.79%	7.34%	NA
Japonica Intermediate	241	98.30%	0.00%	0.00%	1.66%	NA
VI/Aromatic	96	87.50%	1.00%	6.25%	5.21%	NA
Intermediate	90	66.70%	1.10%	2.22%	30.00%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0222538877	C -> T	LOC_Os02g37270.1	downstream_gene_variant ; 2029.0bp to feature; MODIFIER	silent_mutation	Average:32.758; most accessible tissue: Minghui63 panicle, score: 53.77	N	N	N	N
vg0222538877	C -> T	LOC_Os02g37260-LOC_Os02g37270	intergenic_region ; MODIFIER	silent_mutation	Average:32.758; most accessible tissue: Minghui63 panicle, score: 53.77	N	N	N	N
vg0222538877	C -> DEL	N	N	silent_mutation	Average:32.758; most accessible tissue: Minghui63 panicle, score: 53.77	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0222538877	7.52E-06	NA	mr1164	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