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Detailed information for vg0607374248:

Variant ID: vg0607374248 (JBrowse)	Variation Type: SNP
Chromosome: chr06	Position: 7374248
Reference Allele: T	Alternative Allele: C
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 1.00, others allele: 0.00, population size: 115. )

Flanking Sequence (100 bp) in Reference Genome:

TTAGATTACCCATCCGATTTACGATCTGATTACACCATTGTGTTCATAGCAATTAAATCTTTATAACAAGATCTCACATGACTATATTTTTATGAAAAAA[T/C]
AGAAATTACTTTTATAATATATCTAAATTACTTTTAGATTTCATTAAATTACTTCTTAGTCATAAAATTAATTTAATAAAGCCAGAAAGTAATTTACCTA

Reverse complement sequence

TAGGTAAATTACTTTCTGGCTTTATTAAATTAATTTTATGACTAAGAAGTAATTTAATGAAATCTAAAAGTAATTTAGATATATTATAAAAGTAATTTCT[A/G]
TTTTTTCATAAAAATATAGTCATGTGAGATCTTGTTATAAAGATTTAATTGCTATGAACACAATGGTGTAATCAGATCGTAAATCGGATGGGTAATCTAA

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	52.90%	3.40%	13.14%	30.53%	NA
All Indica	2759	21.90%	5.60%	21.13%	51.40%	NA
All Japonica	1512	98.90%	0.30%	0.60%	0.20%	NA
Aus	269	94.80%	0.00%	4.83%	0.37%	NA
Indica I	595	7.70%	18.00%	17.48%	56.81%	NA
Indica II	465	14.00%	0.90%	19.35%	65.81%	NA
Indica III	913	34.10%	0.00%	25.08%	40.85%	NA
Indica Intermediate	786	23.00%	5.60%	20.36%	51.02%	NA
Temperate Japonica	767	99.00%	0.50%	0.52%	0.00%	NA
Tropical Japonica	504	99.20%	0.00%	0.60%	0.20%	NA
Japonica Intermediate	241	98.30%	0.00%	0.83%	0.83%	NA
VI/Aromatic	96	90.60%	0.00%	6.25%	3.12%	NA
Intermediate	90	65.60%	3.30%	11.11%	20.00%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0607374248	T -> C	LOC_Os06g13390.1	upstream_gene_variant ; 2466.0bp to feature; MODIFIER	silent_mutation	Average:11.146; most accessible tissue: Callus, score: 37.39	N	N	N	N
vg0607374248	T -> C	LOC_Os06g13410.1	downstream_gene_variant ; 2038.0bp to feature; MODIFIER	silent_mutation	Average:11.146; most accessible tissue: Callus, score: 37.39	N	N	N	N
vg0607374248	T -> C	LOC_Os06g13420.1	downstream_gene_variant ; 4450.0bp to feature; MODIFIER	silent_mutation	Average:11.146; most accessible tissue: Callus, score: 37.39	N	N	N	N
vg0607374248	T -> C	LOC_Os06g13390-LOC_Os06g13410	intergenic_region ; MODIFIER	silent_mutation	Average:11.146; most accessible tissue: Callus, score: 37.39	N	N	N	N
vg0607374248	T -> DEL	N	N	silent_mutation	Average:11.146; most accessible tissue: Callus, score: 37.39	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0607374248	2.95E-06	3.01E-06	mr1728_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