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Detailed information for vg0207033923:

Variant ID: vg0207033923 (JBrowse)	Variation Type: SNP
Chromosome: chr02	Position: 7033923
Reference Allele: C	Alternative Allele: T
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.67, T: 0.33, others allele: 0.00, population size: 241. )

Flanking Sequence (100 bp) in Reference Genome:

TTTGAACTTCATTGTTCATGAAAATACTACTCCCTCAGGTCAATATTAGCAAATTCTACTAAGCGCAAGTCAATTCCACTGTCTGAAACATCATATATTT[C/T]
GGTCCGGAGGGAGTAATAGAGTTGTATGCAGCGAAATAGTATTATTCCTTATATAGTTAAAAGTAACTAATTTTGTTAGAACTAACTAGTCAAACATATT

Reverse complement sequence

AATATGTTTGACTAGTTAGTTCTAACAAAATTAGTTACTTTTAACTATATAAGGAATAATACTATTTCGCTGCATACAACTCTATTACTCCCTCCGGACC[G/A]
AAATATATGATGTTTCAGACAGTGGAATTGACTTGCGCTTAGTAGAATTTGCTAATATTGACCTGAGGGAGTAGTATTTTCATGAACAATGAAGTTCAAA

Allele Frequencies:

Populations	Population Size	Frequency of T(primary allele)	Frequency of C(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	55.20%	44.30%	0.40%	0.06%	NA
All Indica	2759	79.20%	20.10%	0.62%	0.07%	NA
All Japonica	1512	3.20%	96.80%	0.00%	0.00%	NA
Aus	269	97.40%	2.60%	0.00%	0.00%	NA
Indica I	595	71.90%	27.40%	0.67%	0.00%	NA
Indica II	465	89.00%	10.10%	0.86%	0.00%	NA
Indica III	913	80.70%	18.90%	0.22%	0.11%	NA
Indica Intermediate	786	77.10%	21.90%	0.89%	0.13%	NA
Temperate Japonica	767	2.20%	97.80%	0.00%	0.00%	NA
Tropical Japonica	504	4.00%	96.00%	0.00%	0.00%	NA
Japonica Intermediate	241	5.00%	95.00%	0.00%	0.00%	NA
VI/Aromatic	96	66.70%	33.30%	0.00%	0.00%	NA
Intermediate	90	55.60%	41.10%	2.22%	1.11%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0207033923	C -> T	LOC_Os02g13200.1	intron_variant ; MODIFIER	silent_mutation	Average:61.599; most accessible tissue: Zhenshan97 flower, score: 77.755	N	N	N	N
vg0207033923	C -> DEL	N	N	silent_mutation	Average:61.599; most accessible tissue: Zhenshan97 flower, score: 77.755	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0207033923	NA	2.37E-17	mr1557	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
vg0207033923	NA	1.13E-18	mr1383_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