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Detailed information for vg0202989092:

Variant ID: vg0202989092 (JBrowse)	Variation Type: SNP
Chromosome: chr02	Position: 2989092
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

CGCCTCCCAGCTGTGAGGGGCCGATGACGTCCTCTGCCGAGCCTGAAGCGAAGTCGAAGTCAGTGATGTCGAAGAGCACGGTGGAAGACAGCAAGCGGTC[C/T]
GACGAGGTCCTAGCATGGTCTAGTGGTGGACCTTGACTCGACGTGCCGGCTGCCTGTGACGAAGCCCCGGTGTACTGCTGGAACTGCGCTGAGTGCGAGG

Reverse complement sequence

CCTCGCACTCAGCGCAGTTCCAGCAGTACACCGGGGCTTCGTCACAGGCAGCCGGCACGTCGAGTCAAGGTCCACCACTAGACCATGCTAGGACCTCGTC[G/A]
GACCGCTTGCTGTCTTCCACCGTGCTCTTCGACATCACTGACTTCGACTTCGCTTCAGGCTCGGCAGAGGACGTCATCGGCCCCTCACAGCTGGGAGGCG

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	99.90%	0.10%	0.00%	0.00%	NA
All Indica	2759	99.90%	0.10%	0.00%	0.00%	NA
All Japonica	1512	100.00%	0.00%	0.00%	0.00%	NA
Aus	269	100.00%	0.00%	0.00%	0.00%	NA
Indica I	595	99.80%	0.20%	0.00%	0.00%	NA
Indica II	465	99.60%	0.40%	0.00%	0.00%	NA
Indica III	913	99.90%	0.10%	0.00%	0.00%	NA
Indica Intermediate	786	100.00%	0.00%	0.00%	0.00%	NA
Temperate Japonica	767	100.00%	0.00%	0.00%	0.00%	NA
Tropical Japonica	504	100.00%	0.00%	0.00%	0.00%	NA
Japonica Intermediate	241	100.00%	0.00%	0.00%	0.00%	NA
VI/Aromatic	96	99.00%	1.00%	0.00%	0.00%	NA
Intermediate	90	100.00%	0.00%	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
vg0202989092	C -> T	LOC_Os02g05990.1	synonymous_variant ; p.Ser554Ser; LOW	N	Average:42.357; most accessible tissue: Minghui63 young leaf, score: 72.408	N	N	N	N
vg0202989092	C -> T	LOC_Os02g06000.1	downstream_gene_variant ; 3081.0bp to feature; MODIFIER	N	Average:42.357; most accessible tissue: Minghui63 young leaf, score: 72.408	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0202989092	6.30E-06	NA	mr1961_2	All	Not	Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0202989092	1.07E-07	9.39E-06	mr1961_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