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Detailed information for vg0210614424:

Variant ID: vg0210614424 (JBrowse)	Variation Type: SNP
Chromosome: chr02	Position: 10614424
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: 117. )

Flanking Sequence (100 bp) in Reference Genome:

TTTTCTCTATACTCCTCTCTCACATAATCTAAGCTTACCTGTTAATTTGCAGAGGAGATTTCCAGAATCAGTCAAGCAATGCAAGCTACGTATCCACATA[C/T]
ATGTGCAACCGCTCTTCTCTGTTAGACTTATCTTGGCGTGTGACATATCTTGGCATGCATATGATACCTAAGGCCTATAACCACAATTGGTGAGTGAGAA

Reverse complement sequence

TTCTCACTCACCAATTGTGGTTATAGGCCTTAGGTATCATATGCATGCCAAGATATGTCACACGCCAAGATAAGTCTAACAGAGAAGAGCGGTTGCACAT[G/A]
TATGTGGATACGTAGCTTGCATTGCTTGACTGATTCTGGAAATCTCCTCTGCAAATTAACAGGTAAGCTTAGATTATGTGAGAGAGGAGTATAGAGAAAA

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	66.50%	33.30%	0.13%	0.00%	NA
All Indica	2759	48.40%	51.40%	0.18%	0.00%	NA
All Japonica	1512	99.20%	0.80%	0.00%	0.00%	NA
Aus	269	52.40%	47.60%	0.00%	0.00%	NA
Indica I	595	52.30%	47.70%	0.00%	0.00%	NA
Indica II	465	44.10%	55.30%	0.65%	0.00%	NA
Indica III	913	51.50%	48.50%	0.00%	0.00%	NA
Indica Intermediate	786	44.50%	55.20%	0.25%	0.00%	NA
Temperate Japonica	767	99.50%	0.50%	0.00%	0.00%	NA
Tropical Japonica	504	98.80%	1.20%	0.00%	0.00%	NA
Japonica Intermediate	241	99.20%	0.80%	0.00%	0.00%	NA
VI/Aromatic	96	97.90%	2.10%	0.00%	0.00%	NA
Intermediate	90	82.20%	16.70%	1.11%	0.00%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0210614424	C -> T	LOC_Os02g18290.1	upstream_gene_variant ; 4334.0bp to feature; MODIFIER	silent_mutation	Average:57.545; most accessible tissue: Zhenshan97 flower, score: 67.236	N	N	N	N
vg0210614424	C -> T	LOC_Os02g18300.1	upstream_gene_variant ; 3381.0bp to feature; MODIFIER	silent_mutation	Average:57.545; most accessible tissue: Zhenshan97 flower, score: 67.236	N	N	N	N
vg0210614424	C -> T	LOC_Os02g18290-LOC_Os02g18300	intergenic_region ; MODIFIER	silent_mutation	Average:57.545; most accessible tissue: Zhenshan97 flower, score: 67.236	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0210614424	NA	4.60E-08	mr1722_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