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Detailed information for vg0105159820:

Variant ID: vg0105159820 (JBrowse)	Variation Type: SNP
Chromosome: chr01	Position: 5159820
Reference Allele: C	Alternative Allele: A
Primary Allele: C	Secondary Allele: A

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, others allele: 0.00, population size: 63. )

Flanking Sequence (100 bp) in Reference Genome:

TGAGACCCAGTTTCTTCCTCTCTTCACTTTCTCTCTTAATTAATATAGTGCCACATAAGTTAAAAGTCCTACATGGCAATGTAGTTAATACCATAGACAC[C/A]
ATCCTATGTGGAGGGTTGGGACTGCCCTAAAGCTACAACCAACTAAATCCTAAAACTCAACATGCAAAAGTGCAACATTATCATCCATTAGCAATTATTA

Reverse complement sequence

TAATAATTGCTAATGGATGATAATGTTGCACTTTTGCATGTTGAGTTTTAGGATTTAGTTGGTTGTAGCTTTAGGGCAGTCCCAACCCTCCACATAGGAT[G/T]
GTGTCTATGGTATTAACTACATTGCCATGTAGGACTTTTAACTTATGTGGCACTATATTAATTAAGAGAGAAAGTGAAGAGAGGAAGAAACTGGGTCTCA

Allele Frequencies:

Populations	Population Size	Frequency of C(primary allele)	Frequency of A(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	74.70%	14.20%	0.68%	10.41%	NA
All Indica	2759	80.10%	19.00%	0.18%	0.69%	NA
All Japonica	1512	67.00%	1.10%	1.65%	30.29%	NA
Aus	269	52.80%	46.50%	0.37%	0.37%	NA
Indica I	595	47.20%	52.10%	0.17%	0.50%	NA
Indica II	465	97.40%	1.70%	0.22%	0.65%	NA
Indica III	913	97.30%	2.20%	0.11%	0.44%	NA
Indica Intermediate	786	74.90%	23.70%	0.25%	1.15%	NA
Temperate Japonica	767	85.30%	0.10%	0.26%	14.34%	NA
Tropical Japonica	504	33.70%	2.80%	4.37%	59.13%	NA
Japonica Intermediate	241	78.40%	0.40%	0.41%	20.75%	NA
VI/Aromatic	96	85.40%	3.10%	0.00%	11.46%	NA
Intermediate	90	90.00%	5.60%	1.11%	3.33%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0105159820	C -> A	LOC_Os01g09930.1	upstream_gene_variant ; 3471.0bp to feature; MODIFIER	silent_mutation	Average:27.908; most accessible tissue: Callus, score: 36.365	N	N	N	N
vg0105159820	C -> A	LOC_Os01g09900-LOC_Os01g09930	intergenic_region ; MODIFIER	silent_mutation	Average:27.908; most accessible tissue: Callus, score: 36.365	N	N	N	N
vg0105159820	C -> DEL	N	N	silent_mutation	Average:27.908; most accessible tissue: Callus, score: 36.365	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0105159820	NA	3.02E-06	mr1048	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
vg0105159820	NA	3.44E-06	mr1316	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
vg0105159820	NA	3.92E-06	mr1351	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
vg0105159820	NA	6.00E-06	mr1394	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
vg0105159820	NA	4.43E-06	mr1427	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
vg0105159820	NA	1.11E-08	mr1445	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
vg0105159820	NA	7.20E-06	mr1470	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
vg0105159820	NA	3.26E-08	mr1485	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
vg0105159820	1.69E-06	1.69E-06	mr1485	Ind_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
vg0105159820	NA	2.03E-06	mr1511	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
vg0105159820	NA	5.50E-06	mr1564	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
vg0105159820	NA	4.35E-08	mr1574	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
vg0105159820	NA	1.46E-06	mr1600	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
vg0105159820	NA	3.95E-06	mr1629	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
vg0105159820	NA	2.11E-06	mr1774	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
vg0105159820	NA	2.58E-06	mr1888	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
vg0105159820	NA	1.05E-06	mr1988	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
vg0105159820	NA	7.56E-06	mr1814_2	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