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Detailed information for vg0232851006:

Variant ID: vg0232851006 (JBrowse)	Variation Type: SNP
Chromosome: chr02	Position: 32851006
Reference Allele: G	Alternative Allele: T
Primary Allele: G	Secondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

GAAGCACCTCAATCCTACCCGATATCATACATCAAGCTGCGTTGCCGGAATCGGCTCTATCGGCTTACCTAGTCTGACTCAGACCCAGCCGATCCTAATC[G/T]
TAGCCGATTTGGACTCCAGCCGATTCCTGCTTTGTTTTCGAACTCGATCTCCGCCTTCGATTTTGCTTCGATCTAATCTTCTTTCCTGATGCTGATGTTA

Reverse complement sequence

TAACATCAGCATCAGGAAAGAAGATTAGATCGAAGCAAAATCGAAGGCGGAGATCGAGTTCGAAAACAAAGCAGGAATCGGCTGGAGTCCAAATCGGCTA[C/A]
GATTAGGATCGGCTGGGTCTGAGTCAGACTAGGTAAGCCGATAGAGCCGATTCCGGCAACGCAGCTTGATGTATGATATCGGGTAGGATTGAGGTGCTTC

Allele Frequencies:

Populations	Population Size	Frequency of G(primary allele)	Frequency of T(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	97.10%	2.40%	0.49%	0.00%	NA
All Indica	2759	100.00%	0.00%	0.00%	0.00%	NA
All Japonica	1512	91.30%	7.20%	1.52%	0.00%	NA
Aus	269	100.00%	0.00%	0.00%	0.00%	NA
Indica I	595	100.00%	0.00%	0.00%	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	96.60%	2.30%	1.04%	0.00%	NA
Tropical Japonica	504	87.10%	11.70%	1.19%	0.00%	NA
Japonica Intermediate	241	83.00%	13.30%	3.73%	0.00%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	96.70%	3.30%	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
vg0232851006	G -> T	LOC_Os02g53690-LOC_Os02g53700	intergenic_region ; MODIFIER	silent_mutation	Average:49.766; most accessible tissue: Zhenshan97 panicle, score: 79.071	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0232851006	4.09E-06	4.09E-06	mr1918	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