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Detailed information for vg0917229602:

Variant ID: vg0917229602 (JBrowse)	Variation Type: SNP
Chromosome: chr09	Position: 17229602
Reference Allele: C	Alternative Allele: T
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

GCCATTCCAGTTACGCCTTGCCAAATTATCCTTAGTTAACACAACCCCTTTAAGCAGGTACCACATGAAAATTTTAATTTTAAGTGGCAACTTAAGCTTC[C/T]
AAATACACTTGTTTATCTCGATATAGCCATTATTAATTAAAGCTAGGTACATAGACCTCACCGAGAACAAGCCATTCTGATGGAAATTCCATCTAAATCT

Reverse complement sequence

AGATTTAGATGGAATTTCCATCAGAATGGCTTGTTCTCGGTGAGGTCTATGTACCTAGCTTTAATTAATAATGGCTATATCGAGATAAACAAGTGTATTT[G/A]
GAAGCTTAAGTTGCCACTTAAAATTAAAATTTTCATGTGGTACCTGCTTAAAGGGGTTGTGTTAACTAAGGATAATTTGGCAAGGCGTAACTGGAATGGC

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	62.70%	36.40%	0.99%	0.00%	NA
All Indica	2759	97.70%	2.00%	0.25%	0.00%	NA
All Japonica	1512	0.50%	99.10%	0.40%	0.00%	NA
Aus	269	83.30%	6.30%	10.41%	0.00%	NA
Indica I	595	99.00%	0.70%	0.34%	0.00%	NA
Indica II	465	95.90%	4.10%	0.00%	0.00%	NA
Indica III	913	98.40%	1.40%	0.22%	0.00%	NA
Indica Intermediate	786	97.10%	2.50%	0.38%	0.00%	NA
Temperate Japonica	767	0.10%	99.90%	0.00%	0.00%	NA
Tropical Japonica	504	0.20%	99.00%	0.79%	0.00%	NA
Japonica Intermediate	241	2.50%	96.70%	0.83%	0.00%	NA
VI/Aromatic	96	2.10%	95.80%	2.08%	0.00%	NA
Intermediate	90	34.40%	61.10%	4.44%	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
vg0917229602	C -> T	LOC_Os09g28354.1	downstream_gene_variant ; 641.0bp to feature; MODIFIER	silent_mutation	Average:42.937; most accessible tissue: Zhenshan97 root, score: 73.143	N	N	N	N
vg0917229602	C -> T	LOC_Os09g28370.1	downstream_gene_variant ; 1696.0bp to feature; MODIFIER	silent_mutation	Average:42.937; most accessible tissue: Zhenshan97 root, score: 73.143	N	N	N	N
vg0917229602	C -> T	LOC_Os09g28354-LOC_Os09g28370	intergenic_region ; MODIFIER	silent_mutation	Average:42.937; most accessible tissue: Zhenshan97 root, score: 73.143	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0917229602	4.80E-06	NA	mr1914_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