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Detailed information for vg0601115487:

Variant ID: vg0601115487 (JBrowse)	Variation Type: SNP
Chromosome: chr06	Position: 1115487
Reference Allele: T	Alternative Allele: C
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

TGCATATTTGTCTGAATGTTTATTCAATAACTGTGTATATGCCCCCATTTTTACATGCAGCTTGTATTTTGATAAACTTTTACAAATATGATAATTTTGA[T/C]
AGAATATTAAAATTTTGATATAATTTTGCCACAAATTTGATAAAATTTGGGTATTTTGAAGGAAAAAAAAGATAGAATTTGGGCACAATTTTGGCATGGT

Reverse complement sequence

ACCATGCCAAAATTGTGCCCAAATTCTATCTTTTTTTTCCTTCAAAATACCCAAATTTTATCAAATTTGTGGCAAAATTATATCAAAATTTTAATATTCT[A/G]
TCAAAATTATCATATTTGTAAAAGTTTATCAAAATACAAGCTGCATGTAAAAATGGGGGCATATACACAGTTATTGAATAAACATTCAGACAAATATGCA

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	75.80%	11.00%	7.24%	5.90%	NA
All Indica	2759	65.70%	18.60%	11.34%	4.31%	NA
All Japonica	1512	89.20%	0.20%	0.73%	9.85%	NA
Aus	269	94.10%	0.40%	4.09%	1.49%	NA
Indica I	595	67.10%	3.50%	24.03%	5.38%	NA
Indica II	465	86.90%	2.60%	6.88%	3.66%	NA
Indica III	913	51.20%	38.60%	6.24%	4.05%	NA
Indica Intermediate	786	69.10%	16.40%	10.31%	4.20%	NA
Temperate Japonica	767	99.90%	0.00%	0.13%	0.00%	NA
Tropical Japonica	504	69.40%	0.40%	1.39%	28.77%	NA
Japonica Intermediate	241	96.70%	0.40%	1.24%	1.66%	NA
VI/Aromatic	96	90.60%	1.00%	4.17%	4.17%	NA
Intermediate	90	91.10%	2.20%	3.33%	3.33%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0601115487	T -> C	LOC_Os06g03020.1	upstream_gene_variant ; 4739.0bp to feature; MODIFIER	silent_mutation	Average:24.467; most accessible tissue: Callus, score: 36.934	N	N	N	N
vg0601115487	T -> C	LOC_Os06g03030.1	downstream_gene_variant ; 2297.0bp to feature; MODIFIER	silent_mutation	Average:24.467; most accessible tissue: Callus, score: 36.934	N	N	N	N
vg0601115487	T -> C	LOC_Os06g03040.1	downstream_gene_variant ; 1188.0bp to feature; MODIFIER	silent_mutation	Average:24.467; most accessible tissue: Callus, score: 36.934	N	N	N	N
vg0601115487	T -> C	LOC_Os06g03030-LOC_Os06g03040	intergenic_region ; MODIFIER	silent_mutation	Average:24.467; most accessible tissue: Callus, score: 36.934	N	N	N	N
vg0601115487	T -> DEL	N	N	silent_mutation	Average:24.467; most accessible tissue: Callus, score: 36.934	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0601115487	3.91E-06	NA	Grain_length	Ind_All	YES	Breeding signatures of rice improvement revealed by a genomic variation map from a large germplasm collection, Proc Natl Acad Sci USA, 112(39): E5411-E5419, PMID:26358652