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Detailed information for vg0316245980:

Variant ID: vg0316245980 (JBrowse)	Variation Type: SNP
Chromosome: chr03	Position: 16245980
Reference Allele: A	Alternative Allele: C
Primary Allele: A	Secondary Allele: C

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

GTGTGCTTCCCGTACATAAAAAAACAATTAGATTTTCACAGATCATTTTGGGCAGATAGGCTAGCCTTCCGCACGCAAAATAGGTTTTGGGCCGCCTAGA[A/C]
AAACCTACTAGTGACATATTACAACATCTTAAGAGATACAATCACAGGATCGCAACCAAAAACATTTTCCAACTTTGGCACGCGTACTAATTGGATACCA

Reverse complement sequence

TGGTATCCAATTAGTACGCGTGCCAAAGTTGGAAAATGTTTTTGGTTGCGATCCTGTGATTGTATCTCTTAAGATGTTGTAATATGTCACTAGTAGGTTT[T/G]
TCTAGGCGGCCCAAAACCTATTTTGCGTGCGGAAGGCTAGCCTATCTGCCCAAAATGATCTGTGAAAATCTAATTGTTTTTTTATGTACGGGAAGCACAC

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	85.20%	4.60%	6.71%	3.45%	NA
All Indica	2759	83.00%	0.50%	10.80%	5.73%	NA
All Japonica	1512	91.10%	8.50%	0.46%	0.00%	NA
Aus	269	98.90%	0.40%	0.74%	0.00%	NA
Indica I	595	97.60%	0.00%	2.18%	0.17%	NA
Indica II	465	55.10%	0.20%	29.03%	15.70%	NA
Indica III	913	88.60%	1.00%	6.24%	4.16%	NA
Indica Intermediate	786	81.80%	0.50%	11.83%	5.85%	NA
Temperate Japonica	767	97.10%	2.60%	0.26%	0.00%	NA
Tropical Japonica	504	83.10%	16.10%	0.79%	0.00%	NA
Japonica Intermediate	241	88.40%	11.20%	0.41%	0.00%	NA
VI/Aromatic	96	26.00%	71.90%	1.04%	1.04%	NA
Intermediate	90	77.80%	7.80%	10.00%	4.44%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0316245980	A -> C	LOC_Os03g28230.1	upstream_gene_variant ; 4341.0bp to feature; MODIFIER	silent_mutation	Average:58.113; most accessible tissue: Callus, score: 90.523	N	N	N	N
vg0316245980	A -> C	LOC_Os03g28250.1	upstream_gene_variant ; 1198.0bp to feature; MODIFIER	silent_mutation	Average:58.113; most accessible tissue: Callus, score: 90.523	N	N	N	N
vg0316245980	A -> C	LOC_Os03g28260.1	downstream_gene_variant ; 4641.0bp to feature; MODIFIER	silent_mutation	Average:58.113; most accessible tissue: Callus, score: 90.523	N	N	N	N
vg0316245980	A -> C	LOC_Os03g28230-LOC_Os03g28250	intergenic_region ; MODIFIER	silent_mutation	Average:58.113; most accessible tissue: Callus, score: 90.523	N	N	N	N
vg0316245980	A -> DEL	N	N	silent_mutation	Average:58.113; most accessible tissue: Callus, score: 90.523	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0316245980	4.83E-06	NA	mr1027_2	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