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Detailed information for vg0123309862:

Variant ID: vg0123309862 (JBrowse)	Variation Type: SNP
Chromosome: chr01	Position: 23309862
Reference Allele: C	Alternative Allele: T
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

TAGCATAAGTTACATCCCGAAATTGCTCTAGACCAAGCATACTTAACGTCAAAGTTCTTTGGAGATTGGCTTCCAGAAAAGTAGTTGTAACATGTTGGTA[C/T]
GAGTATTCTATTAATCCTATTATGCCCTAGGCCAGGATGTCAAATTAGAGTTATTAAATGATTTTAAATGGAAAAGTCACCAAAACCAAAGTTGTAGAAC

Reverse complement sequence

GTTCTACAACTTTGGTTTTGGTGACTTTTCCATTTAAAATCATTTAATAACTCTAATTTGACATCCTGGCCTAGGGCATAATAGGATTAATAGAATACTC[G/A]
TACCAACATGTTACAACTACTTTTCTGGAAGCCAATCTCCAAAGAACTTTGACGTTAAGTATGCTTGGTCTAGAGCAATTTCGGGATGTAACTTATGCTA

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	68.00%	10.40%	21.60%	0.02%	NA
All Indica	2759	79.80%	3.90%	16.31%	0.04%	NA
All Japonica	1512	57.80%	23.70%	18.45%	0.00%	NA
Aus	269	12.30%	3.30%	84.39%	0.00%	NA
Indica I	595	80.00%	3.70%	16.30%	0.00%	NA
Indica II	465	93.50%	0.60%	5.81%	0.00%	NA
Indica III	913	73.80%	5.00%	21.14%	0.00%	NA
Indica Intermediate	786	78.40%	4.60%	16.92%	0.13%	NA
Temperate Japonica	767	39.80%	36.00%	24.25%	0.00%	NA
Tropical Japonica	504	91.50%	3.80%	4.76%	0.00%	NA
Japonica Intermediate	241	44.80%	26.60%	28.63%	0.00%	NA
VI/Aromatic	96	44.80%	1.00%	54.17%	0.00%	NA
Intermediate	90	70.00%	15.60%	14.44%	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
vg0123309862	C -> T	LOC_Os01g41170.1	downstream_gene_variant ; 1309.0bp to feature; MODIFIER	silent_mutation	Average:35.092; most accessible tissue: Minghui63 root, score: 57.225	N	N	N	N
vg0123309862	C -> T	LOC_Os01g41180.1	downstream_gene_variant ; 3349.0bp to feature; MODIFIER	silent_mutation	Average:35.092; most accessible tissue: Minghui63 root, score: 57.225	N	N	N	N
vg0123309862	C -> T	LOC_Os01g41160-LOC_Os01g41170	intergenic_region ; MODIFIER	silent_mutation	Average:35.092; most accessible tissue: Minghui63 root, score: 57.225	N	N	N	N
vg0123309862	C -> DEL	N	N	silent_mutation	Average:35.092; most accessible tissue: Minghui63 root, score: 57.225	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0123309862	NA	1.83E-06	mr1131_2	Ind_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
vg0123309862	1.73E-06	1.12E-07	mr1199_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