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Detailed information for vg0319788098:

Variant ID: vg0319788098 (JBrowse)	Variation Type: SNP
Chromosome: chr03	Position: 19788098
Reference Allele: T	Alternative Allele: C
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

AGATCATACGATCAATAATACACTCGGTGGATCAATCCCCGGACAGGAGTAGGGTATTACTTCTTGATTAAGAAGGCCTGAACCTGTATAAAATTCCTTG[T/C]
CTCTTTACCCATCCACTTTTCTAGCTTGATAGCCACCCCCTTTTAGTATTGCCGAAATCTTGTTTCGACACTGAACGACCCTCATCACCCTAAGCCTTGT

Reverse complement sequence

ACAAGGCTTAGGGTGATGAGGGTCGTTCAGTGTCGAAACAAGATTTCGGCAATACTAAAAGGGGGTGGCTATCAAGCTAGAAAAGTGGATGGGTAAAGAG[A/G]
CAAGGAATTTTATACAGGTTCAGGCCTTCTTAATCAAGAAGTAATACCCTACTCCTGTCCGGGGATTGATCCACCGAGTGTATTATTGATCGTATGATCT

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	96.70%	2.70%	0.36%	0.19%	NA
All Indica	2759	99.70%	0.00%	0.07%	0.25%	NA
All Japonica	1512	90.70%	8.50%	0.79%	0.00%	NA
Aus	269	100.00%	0.00%	0.00%	0.00%	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	99.80%	0.00%	0.00%	0.22%	NA
Indica Intermediate	786	99.10%	0.00%	0.25%	0.64%	NA
Temperate Japonica	767	97.30%	2.30%	0.39%	0.00%	NA
Tropical Japonica	504	83.70%	14.70%	1.59%	0.00%	NA
Japonica Intermediate	241	84.60%	14.90%	0.41%	0.00%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	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
vg0319788098	T -> C	LOC_Os03g35720.1	upstream_gene_variant ; 1439.0bp to feature; MODIFIER	silent_mutation	Average:47.689; most accessible tissue: Minghui63 panicle, score: 64.459	N	N	N	N
vg0319788098	T -> C	LOC_Os03g35720-LOC_Os03g35730	intergenic_region ; MODIFIER	silent_mutation	Average:47.689; most accessible tissue: Minghui63 panicle, score: 64.459	N	N	N	N
vg0319788098	T -> DEL	N	N	silent_mutation	Average:47.689; most accessible tissue: Minghui63 panicle, score: 64.459	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0319788098	NA	1.77E-06	mr1179	Jap_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
vg0319788098	9.99E-07	9.98E-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
vg0319788098	NA	5.28E-06	mr1836_2	Jap_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