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Detailed information for vg0202628743:

Variant ID: vg0202628743 (JBrowse)	Variation Type: SNP
Chromosome: chr02	Position: 2628743
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: 309. )

Flanking Sequence (100 bp) in Reference Genome:

CAATTTCAACCAAACTTCCAATTTTGGCGTGAACTAAGGCAGTGTTTAGTTCCCCCAAATTCCCAGCTTTCCATCACATCATATCACATCGAAAACTTTC[C/T]
TACACACATAAACTACCAACTTTTTCTCTAAACTACCAACTTTCTTTCAACTTCCTAACTTTTTCACCATCTAAACACAGCCTAAACACACCTCAAGTCC

Reverse complement sequence

GGACTTGAGGTGTGTTTAGGCTGTGTTTAGATGGTGAAAAAGTTAGGAAGTTGAAAGAAAGTTGGTAGTTTAGAGAAAAAGTTGGTAGTTTATGTGTGTA[G/A]
GAAAGTTTTCGATGTGATATGATGTGATGGAAAGCTGGGAATTTGGGGGAACTAAACACTGCCTTAGTTCACGCCAAAATTGGAAGTTTGGTTGAAATTG

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	98.80%	1.00%	0.23%	0.00%	NA
All Indica	2759	100.00%	0.00%	0.04%	0.00%	NA
All Japonica	1512	96.40%	3.00%	0.66%	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	100.00%	0.00%	0.00%	0.00%	NA
Indica III	913	100.00%	0.00%	0.00%	0.00%	NA
Indica Intermediate	786	100.00%	0.00%	0.00%	0.00%	NA
Temperate Japonica	767	96.20%	2.60%	1.17%	0.00%	NA
Tropical Japonica	504	95.40%	4.40%	0.20%	0.00%	NA
Japonica Intermediate	241	98.80%	1.20%	0.00%	0.00%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	98.90%	1.10%	0.00%	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
vg0202628743	C -> T	LOC_Os02g05450.1	downstream_gene_variant ; 2433.0bp to feature; MODIFIER	silent_mutation	Average:50.631; most accessible tissue: Minghui63 panicle, score: 76.913	N	N	N	N
vg0202628743	C -> T	LOC_Os02g05460.1	downstream_gene_variant ; 2997.0bp to feature; MODIFIER	silent_mutation	Average:50.631; most accessible tissue: Minghui63 panicle, score: 76.913	N	N	N	N
vg0202628743	C -> T	LOC_Os02g05450-LOC_Os02g05460	intergenic_region ; MODIFIER	silent_mutation	Average:50.631; most accessible tissue: Minghui63 panicle, score: 76.913	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0202628743	3.82E-06	NA	mr1517	Jap_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