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Detailed information for vg0306548970:

Variant ID: vg0306548970 (JBrowse)	Variation Type: SNP
Chromosome: chr03	Position: 6548970
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

TTTCGGAGCCCGAAGACCCGCAGTGCGAGGATTTCGAGGATCAAGCTCCAGATCTCGAGCAAGGCAAGCCACCCTTGAACATCTTGAGCCTATATTTGAA[C/T]
TTAATTATATTGCTTGCAAAATATCATGCATTGATAGGATTGCACGTAATATGTTTGCCCCGTCTGCGAGGCAGATTAGTGGGCATACCTAACTTGTTGC

Reverse complement sequence

GCAACAAGTTAGGTATGCCCACTAATCTGCCTCGCAGACGGGGCAAACATATTACGTGCAATCCTATCAATGCATGATATTTTGCAAGCAATATAATTAA[G/A]
TTCAAATATAGGCTCAAGATGTTCAAGGGTGGCTTGCCTTGCTCGAGATCTGGAGCTTGATCCTCGAAATCCTCGCACTGCGGGTCTTCGGGCTCCGAAA

Allele Frequencies:

Populations	Population Size	Frequency of C(primary allele)	Frequency of T(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	33.00%	3.70%	7.51%	55.82%	NA
All Indica	2759	1.90%	2.50%	10.26%	85.32%	NA
All Japonica	1512	96.20%	0.00%	0.07%	3.70%	NA
Aus	269	0.70%	38.30%	20.45%	40.52%	NA
Indica I	595	1.70%	0.00%	8.91%	89.41%	NA
Indica II	465	2.60%	1.90%	8.17%	87.31%	NA
Indica III	913	1.20%	3.00%	12.16%	83.68%	NA
Indica Intermediate	786	2.40%	4.30%	10.31%	82.95%	NA
Temperate Japonica	767	97.10%	0.00%	0.00%	2.87%	NA
Tropical Japonica	504	94.00%	0.00%	0.20%	5.75%	NA
Japonica Intermediate	241	97.90%	0.00%	0.00%	2.07%	NA
VI/Aromatic	96	9.40%	0.00%	9.38%	81.25%	NA
Intermediate	90	45.60%	1.10%	7.78%	45.56%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0306548970	C -> T	LOC_Os03g12390.1	upstream_gene_variant ; 2492.0bp to feature; MODIFIER	silent_mutation	Average:5.537; most accessible tissue: Callus, score: 9.566	N	N	N	N
vg0306548970	C -> T	LOC_Os03g12400.1	upstream_gene_variant ; 1295.0bp to feature; MODIFIER	silent_mutation	Average:5.537; most accessible tissue: Callus, score: 9.566	N	N	N	N
vg0306548970	C -> T	LOC_Os03g12400-LOC_Os03g12414	intergenic_region ; MODIFIER	silent_mutation	Average:5.537; most accessible tissue: Callus, score: 9.566	N	N	N	N
vg0306548970	C -> DEL	N	N	silent_mutation	Average:5.537; most accessible tissue: Callus, score: 9.566	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0306548970	1.43E-06	1.43E-06	mr1341_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
vg0306548970	NA	4.38E-06	mr1992_2	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