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Detailed information for vg0316846972:

Variant ID: vg0316846972 (JBrowse)	Variation Type: SNP
Chromosome: chr03	Position: 16846972
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

ACTTCCTCCTATATAAAACCATTTAGAAAAGCACTTTTCACATCCATTTGATACAATTTAAAACCTTTTGAAGCAGCAAAAGCCAACAAAAGTCTAATTG[C/T]
CTCAATTCTAGCAACAGGAGCAAAAGTTTCATAAAAATCCAAACCCTCAACTTAAGTAAAACCTTCAGCAACAAGTCTAGCTTTATTTCTCACAATCAAA

Reverse complement sequence

TTTGATTGTGAGAAATAAAGCTAGACTTGTTGCTGAAGGTTTTACTTAAGTTGAGGGTTTGGATTTTTATGAAACTTTTGCTCCTGTTGCTAGAATTGAG[G/A]
CAATTAGACTTTTGTTGGCTTTTGCTGCTTCAAAAGGTTTTAAATTGTATCAAATGGATGTGAAAAGTGCTTTTCTAAATGGTTTTATATAGGAGGAAGT

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	95.40%	2.70%	0.53%	1.35%	NA
All Indica	2759	99.50%	0.30%	0.11%	0.07%	NA
All Japonica	1512	91.10%	7.60%	1.19%	0.13%	NA
Aus	269	98.90%	0.70%	0.00%	0.37%	NA
Indica I	595	100.00%	0.00%	0.00%	0.00%	NA
Indica II	465	100.00%	0.00%	0.00%	0.00%	NA
Indica III	913	98.90%	0.80%	0.11%	0.22%	NA
Indica Intermediate	786	99.60%	0.10%	0.25%	0.00%	NA
Temperate Japonica	767	96.00%	3.00%	1.04%	0.00%	NA
Tropical Japonica	504	89.70%	9.30%	0.99%	0.00%	NA
Japonica Intermediate	241	78.40%	18.70%	2.07%	0.83%	NA
VI/Aromatic	96	37.50%	2.10%	1.04%	59.38%	NA
Intermediate	90	94.40%	0.00%	3.33%	2.22%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0316846972	C -> T	LOC_Os03g29550.1	upstream_gene_variant ; 4199.0bp to feature; MODIFIER	silent_mutation	Average:17.429; most accessible tissue: Minghui63 panicle, score: 34.226	N	N	N	N
vg0316846972	C -> T	LOC_Os03g29560.1	intron_variant ; MODIFIER	silent_mutation	Average:17.429; most accessible tissue: Minghui63 panicle, score: 34.226	N	N	N	N
vg0316846972	C -> DEL	N	N	silent_mutation	Average:17.429; most accessible tissue: Minghui63 panicle, score: 34.226	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0316846972	4.16E-07	4.16E-07	mr1610_2	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