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Detailed information for vg0315010554:

Variant ID: vg0315010554 (JBrowse)	Variation Type: SNP
Chromosome: chr03	Position: 15010554
Reference Allele: A	Alternative Allele: C
Primary Allele: A	Secondary Allele: C

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

TTAAAAAATAATTTGAATTTTTGATAAATTTTGTACGGTTTCGTACGGTTTTTCACGGTTACCACGGTTAATGCGCGGTAACCGTGCTTACCGCCAGGGC[A/C]
CGGTAACCCCGGTCCCGGCGGTTTGGGAAACCCTGATTCCGAGGTAACTCGGTAAAGCCGCTTGCACAGTTTTGCATTGTAAATGCCCTGATCGAGTTGC

Reverse complement sequence

GCAACTCGATCAGGGCATTTACAATGCAAAACTGTGCAAGCGGCTTTACCGAGTTACCTCGGAATCAGGGTTTCCCAAACCGCCGGGACCGGGGTTACCG[T/G]
GCCCTGGCGGTAAGCACGGTTACCGCGCATTAACCGTGGTAACCGTGAAAAACCGTACGAAACCGTACAAAATTTATCAAAAATTCAAATTATTTTTTAA

Allele Frequencies:

Populations	Population Size	Frequency of A(primary allele)	Frequency of C(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	94.90%	5.10%	0.00%	0.00%	NA
All Indica	2759	99.60%	0.40%	0.00%	0.00%	NA
All Japonica	1512	88.80%	11.20%	0.00%	0.00%	NA
Aus	269	100.00%	0.00%	0.00%	0.00%	NA
Indica I	595	99.80%	0.20%	0.00%	0.00%	NA
Indica II	465	100.00%	0.00%	0.00%	0.00%	NA
Indica III	913	98.90%	1.10%	0.00%	0.00%	NA
Indica Intermediate	786	100.00%	0.00%	0.00%	0.00%	NA
Temperate Japonica	767	94.10%	5.90%	0.00%	0.00%	NA
Tropical Japonica	504	87.90%	12.10%	0.00%	0.00%	NA
Japonica Intermediate	241	73.40%	26.60%	0.00%	0.00%	NA
VI/Aromatic	96	43.80%	56.20%	0.00%	0.00%	NA
Intermediate	90	92.20%	7.80%	0.00%	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
vg0315010554	A -> C	LOC_Os03g26240.1	upstream_gene_variant ; 1101.0bp to feature; MODIFIER	silent_mutation	Average:71.481; most accessible tissue: Callus, score: 84.248	N	N	N	N
vg0315010554	A -> C	LOC_Os03g26250.1	upstream_gene_variant ; 608.0bp to feature; MODIFIER	silent_mutation	Average:71.481; most accessible tissue: Callus, score: 84.248	N	N	N	N
vg0315010554	A -> C	LOC_Os03g26229.1	downstream_gene_variant ; 2294.0bp to feature; MODIFIER	silent_mutation	Average:71.481; most accessible tissue: Callus, score: 84.248	N	N	N	N
vg0315010554	A -> C	LOC_Os03g26240-LOC_Os03g26250	intergenic_region ; MODIFIER	silent_mutation	Average:71.481; most accessible tissue: Callus, score: 84.248	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0315010554	9.11E-07	9.11E-07	mr1595	Jap_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