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Detailed information for vg0142802503:

Variant ID: vg0142802503 (JBrowse)	Variation Type: SNP
Chromosome: chr01	Position: 42802503
Reference Allele: A	Alternative Allele: C
Primary Allele: A	Secondary Allele: C

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.76, A: 0.24, others allele: 0.00, population size: 222. )

Flanking Sequence (100 bp) in Reference Genome:

TTCTCGCGCGTCTGCACGAGCTAGGCATTCTCGAAATTTTATGGTCATTATAAAATATCCCAAGGTATCTCAAGTTACTTAACTAGAAAAAGTGCCCGTG[A/C]
TTTGTAACGGGAAGTGTAAAGATCAGAAAATTAAGGAAAAGTTGAGAAAGATTTACATTAGAGTAAAGTGCATTGGCGGTCCTTAATCTTGTAGGGTTGT

Reverse complement sequence

ACAACCCTACAAGATTAAGGACCGCCAATGCACTTTACTCTAATGTAAATCTTTCTCAACTTTTCCTTAATTTTCTGATCTTTACACTTCCCGTTACAAA[T/G]
CACGGGCACTTTTTCTAGTTAAGTAACTTGAGATACCTTGGGATATTTTATAATGACCATAAAATTTCGAGAATGCCTAGCTCGTGCAGACGCGCGAGAA

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	80.60%	19.40%	0.04%	0.00%	NA
All Indica	2759	75.90%	24.00%	0.07%	0.00%	NA
All Japonica	1512	93.10%	6.90%	0.00%	0.00%	NA
Aus	269	50.90%	49.10%	0.00%	0.00%	NA
Indica I	595	72.80%	26.90%	0.34%	0.00%	NA
Indica II	465	97.00%	3.00%	0.00%	0.00%	NA
Indica III	913	63.20%	36.80%	0.00%	0.00%	NA
Indica Intermediate	786	80.70%	19.30%	0.00%	0.00%	NA
Temperate Japonica	767	99.90%	0.10%	0.00%	0.00%	NA
Tropical Japonica	504	80.00%	20.00%	0.00%	0.00%	NA
Japonica Intermediate	241	98.80%	1.20%	0.00%	0.00%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	81.10%	18.90%	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
vg0142802503	A -> C	LOC_Os01g73860.1	upstream_gene_variant ; 3013.0bp to feature; MODIFIER	silent_mutation	Average:58.977; most accessible tissue: Minghui63 panicle, score: 84.552	N	N	N	N
vg0142802503	A -> C	LOC_Os01g73870.1	upstream_gene_variant ; 2399.0bp to feature; MODIFIER	silent_mutation	Average:58.977; most accessible tissue: Minghui63 panicle, score: 84.552	N	N	N	N
vg0142802503	A -> C	LOC_Os01g73860-LOC_Os01g73870	intergenic_region ; MODIFIER	silent_mutation	Average:58.977; most accessible tissue: Minghui63 panicle, score: 84.552	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0142802503	NA	9.92E-06	mr1070	Ind_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
vg0142802503	NA	7.41E-08	mr1180	Ind_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
vg0142802503	NA	2.77E-06	mr1280	Ind_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
vg0142802503	NA	4.35E-06	mr1534	Ind_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
vg0142802503	NA	2.06E-06	mr1627	Ind_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
vg0142802503	4.67E-06	NA	mr1788	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
vg0142802503	NA	2.13E-07	mr1839	Ind_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
vg0142802503	NA	2.64E-06	mr1277_2	Ind_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
vg0142802503	NA	7.43E-06	mr1332_2	Ind_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