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Detailed information for vg0142370628:

Variant ID: vg0142370628 (JBrowse)	Variation Type: SNP
Chromosome: chr01	Position: 42370628
Reference Allele: T	Alternative Allele: A
Primary Allele: T	Secondary Allele: A

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.90, T: 0.10, others allele: 0.00, population size: 111. )

Flanking Sequence (100 bp) in Reference Genome:

CCCCTTAATATTTTCTTGTGCGTTCATTTGATTTTTTTTATTTCAGTTTGCTGATCTTGATTTATCTGTATGTAATCGTATTCAACCTTAACTACCAAAA[T/A]
GGTTAAGAATACACTATATATTGGCACTTTGGCAGATCTCTGAACTTCGAATTCAGAGGTTAACAAAAACAGGAAGGGGTGAATTATGCATAGATCGAGC

Reverse complement sequence

GCTCGATCTATGCATAATTCACCCCTTCCTGTTTTTGTTAACCTCTGAATTCGAAGTTCAGAGATCTGCCAAAGTGCCAATATATAGTGTATTCTTAACC[A/T]
TTTTGGTAGTTAAGGTTGAATACGATTACATACAGATAAATCAAGATCAGCAAACTGAAATAAAAAAAATCAAATGAACGCACAAGAAAATATTAAGGGG

Allele Frequencies:

Populations	Population Size	Frequency of T(primary allele)	Frequency of A(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	61.20%	38.50%	0.21%	0.11%	NA
All Indica	2759	61.80%	37.70%	0.33%	0.18%	NA
All Japonica	1512	56.30%	43.70%	0.00%	0.00%	NA
Aus	269	77.70%	22.30%	0.00%	0.00%	NA
Indica I	595	70.90%	28.70%	0.00%	0.34%	NA
Indica II	465	24.70%	74.00%	1.08%	0.22%	NA
Indica III	913	70.90%	28.70%	0.22%	0.22%	NA
Indica Intermediate	786	66.30%	33.50%	0.25%	0.00%	NA
Temperate Japonica	767	77.60%	22.40%	0.00%	0.00%	NA
Tropical Japonica	504	27.40%	72.60%	0.00%	0.00%	NA
Japonica Intermediate	241	49.00%	51.00%	0.00%	0.00%	NA
VI/Aromatic	96	76.00%	24.00%	0.00%	0.00%	NA
Intermediate	90	60.00%	38.90%	1.11%	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
vg0142370628	T -> A	LOC_Os01g73024.1	downstream_gene_variant ; 263.0bp to feature; MODIFIER	silent_mutation	Average:38.468; most accessible tissue: Zhenshan97 root, score: 57.64	N	N	N	N
vg0142370628	T -> A	LOC_Os01g73024-LOC_Os01g73040	intergenic_region ; MODIFIER	silent_mutation	Average:38.468; most accessible tissue: Zhenshan97 root, score: 57.64	N	N	N	N
vg0142370628	T -> DEL	N	N	silent_mutation	Average:38.468; most accessible tissue: Zhenshan97 root, score: 57.64	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0142370628	7.02E-07	7.02E-07	mr1193	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
vg0142370628	NA	7.28E-07	mr1974	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
vg0142370628	NA	9.08E-06	mr1322_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
vg0142370628	NA	1.21E-07	mr1336_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
vg0142370628	NA	1.23E-06	mr1438_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