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Detailed information for vg0611857510:

Variant ID: vg0611857510 (JBrowse)	Variation Type: SNP
Chromosome: chr06	Position: 11857510
Reference Allele: C	Alternative Allele: T
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

CTACTTAACTCCAGTGCAGGTCCAAAACTCGCCTTCGGATGTATGAGCGAGCCAGTTGATTTGATCCTATAATCAACAAGAAATAAAGACAAAGGAACCG[C/T]
GGTTAAGTCTATAAATGATAGCCGATCGGTCAGATGCCGATGACATATCGATCGGCAATCATGAATAAGTAAAGAAAAACTAAACCTACTTGATCGGCTG

Reverse complement sequence

CAGCCGATCAAGTAGGTTTAGTTTTTCTTTACTTATTCATGATTGCCGATCGATATGTCATCGGCATCTGACCGATCGGCTATCATTTATAGACTTAACC[G/A]
CGGTTCCTTTGTCTTTATTTCTTGTTGATTATAGGATCAAATCAACTGGCTCGCTCATACATCCGAAGGCGAGTTTTGGACCTGCACTGGAGTTAAGTAG

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	65.10%	32.50%	2.45%	0.00%	NA
All Indica	2759	94.10%	3.90%	1.99%	0.00%	NA
All Japonica	1512	11.50%	88.50%	0.00%	0.00%	NA
Aus	269	90.70%	8.20%	1.12%	0.00%	NA
Indica I	595	92.90%	3.20%	3.87%	0.00%	NA
Indica II	465	96.10%	3.70%	0.22%	0.00%	NA
Indica III	913	95.80%	3.10%	1.10%	0.00%	NA
Indica Intermediate	786	91.70%	5.60%	2.67%	0.00%	NA
Temperate Japonica	767	3.50%	96.50%	0.00%	0.00%	NA
Tropical Japonica	504	24.00%	76.00%	0.00%	0.00%	NA
Japonica Intermediate	241	10.80%	89.20%	0.00%	0.00%	NA
VI/Aromatic	96	16.70%	31.20%	52.08%	0.00%	NA
Intermediate	90	51.10%	40.00%	8.89%	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
vg0611857510	C -> T	LOC_Os06g20590.1	upstream_gene_variant ; 1638.0bp to feature; MODIFIER	silent_mutation	Average:17.26; most accessible tissue: Callus, score: 22.012	N	N	N	N
vg0611857510	C -> T	LOC_Os06g20600.1	upstream_gene_variant ; 184.0bp to feature; MODIFIER	silent_mutation	Average:17.26; most accessible tissue: Callus, score: 22.012	N	N	N	N
vg0611857510	C -> T	LOC_Os06g20600-LOC_Os06g20610	intergenic_region ; MODIFIER	silent_mutation	Average:17.26; most accessible tissue: Callus, score: 22.012	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0611857510	2.09E-08	NA	mr1033_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