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Detailed information for vg0209279511:

Variant ID: vg0209279511 (JBrowse)	Variation Type: SNP
Chromosome: chr02	Position: 9279511
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

CGTGACAAGACCCTCCACATAACCCTCCCCTAACCATCCACACCACGCTAAGGTTTCACCCCCACCCCTAACGGGCAGTGGGCAGTCCCCTCGTGCGCCG[C/T]
GGTGAATCCGGCAGCTGGACAACCGGACACCCCGGCCGACCCAACTCCATCACGCCCACCCACGCCACCGGTGCCTAGGAAAGGGTCGAGCTATACTTCA

Reverse complement sequence

TGAAGTATAGCTCGACCCTTTCCTAGGCACCGGTGGCGTGGGTGGGCGTGATGGAGTTGGGTCGGCCGGGGTGTCCGGTTGTCCAGCTGCCGGATTCACC[G/A]
CGGCGCACGAGGGGACTGCCCACTGCCCGTTAGGGGTGGGGGTGAAACCTTAGCGTGGTGTGGATGGTTAGGGGAGGGTTATGTGGAGGGTCTTGTCACG

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	93.90%	0.00%	0.30%	5.82%	NA
All Indica	2759	90.00%	0.00%	0.47%	9.50%	NA
All Japonica	1512	99.60%	0.00%	0.07%	0.33%	NA
Aus	269	98.10%	0.00%	0.00%	1.86%	NA
Indica I	595	91.90%	0.00%	0.50%	7.56%	NA
Indica II	465	92.70%	0.00%	0.00%	7.31%	NA
Indica III	913	86.40%	0.00%	0.55%	13.03%	NA
Indica Intermediate	786	91.10%	0.10%	0.64%	8.14%	NA
Temperate Japonica	767	99.70%	0.00%	0.13%	0.13%	NA
Tropical Japonica	504	99.40%	0.00%	0.00%	0.60%	NA
Japonica Intermediate	241	99.60%	0.00%	0.00%	0.41%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	96.70%	0.00%	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
vg0209279511	C -> T	LOC_Os02g16320.1	upstream_gene_variant ; 962.0bp to feature; MODIFIER	silent_mutation	Average:16.262; most accessible tissue: Callus, score: 28.694	N	N	N	N
vg0209279511	C -> T	LOC_Os02g16310.1	downstream_gene_variant ; 761.0bp to feature; MODIFIER	silent_mutation	Average:16.262; most accessible tissue: Callus, score: 28.694	N	N	N	N
vg0209279511	C -> T	LOC_Os02g16310-LOC_Os02g16320	intergenic_region ; MODIFIER	silent_mutation	Average:16.262; most accessible tissue: Callus, score: 28.694	N	N	N	N
vg0209279511	C -> DEL	N	N	silent_mutation	Average:16.262; most accessible tissue: Callus, score: 28.694	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0209279511	3.10E-06	3.10E-06	mr1983_2	Ind_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