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Detailed information for vg0102430888:

Variant ID: vg0102430888 (JBrowse)	Variation Type: SNP
Chromosome: chr01	Position: 2430888
Reference Allele: A	Alternative Allele: T
Primary Allele: T	Secondary Allele: A

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.83, A: 0.19, others allele: 0.00, population size: 59. )

Flanking Sequence (100 bp) in Reference Genome:

GAAATTCGGAATTAAAAATAAGCAATATTGAAAGAAGTTTCCATATAAGAACCCAATACGAGATTAAACCAAATTCGAAATAAAAAAATAAAATCCAAAA[A/T]
TAGAAAAGGAAATGAGAGTCAAGTAGGAATACAATTTTAAAATAGCTGAAATTTGAAATTAAAAATAAGGAATATTAAAAGAAGAGTCCATATATGAACC

Reverse complement sequence

GGTTCATATATGGACTCTTCTTTTAATATTCCTTATTTTTAATTTCAAATTTCAGCTATTTTAAAATTGTATTCCTACTTGACTCTCATTTCCTTTTCTA[T/A]
TTTTGGATTTTATTTTTTTATTTCGAATTTGGTTTAATCTCGTATTGGGTTCTTATATGGAAACTTCTTTCAATATTGCTTATTTTTAATTCCGAATTTC

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	50.20%	12.80%	0.38%	36.63%	NA
All Indica	2759	62.70%	2.10%	0.62%	34.61%	NA
All Japonica	1512	36.20%	22.60%	0.07%	41.20%	NA
Aus	269	13.80%	57.60%	0.00%	28.62%	NA
Indica I	595	34.50%	1.30%	0.17%	64.03%	NA
Indica II	465	90.50%	3.20%	0.00%	6.24%	NA
Indica III	913	63.90%	1.50%	1.42%	33.19%	NA
Indica Intermediate	786	66.30%	2.50%	0.38%	30.79%	NA
Temperate Japonica	767	19.40%	36.60%	0.00%	43.94%	NA
Tropical Japonica	504	67.50%	4.80%	0.00%	27.78%	NA
Japonica Intermediate	241	24.10%	14.90%	0.41%	60.58%	NA
VI/Aromatic	96	12.50%	33.30%	0.00%	54.17%	NA
Intermediate	90	53.30%	20.00%	0.00%	26.67%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0102430888	A -> T	LOC_Os01g05180.1	upstream_gene_variant ; 3905.0bp to feature; MODIFIER	silent_mutation	Average:16.053; most accessible tissue: Minghui63 young leaf, score: 38.036	N	N	N	N
vg0102430888	A -> T	LOC_Os01g05170-LOC_Os01g05180	intergenic_region ; MODIFIER	silent_mutation	Average:16.053; most accessible tissue: Minghui63 young leaf, score: 38.036	N	N	N	N
vg0102430888	A -> DEL	N	N	silent_mutation	Average:16.053; most accessible tissue: Minghui63 young leaf, score: 38.036	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0102430888	NA	4.86E-06	mr1138_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
vg0102430888	6.92E-08	6.91E-08	mr1406_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
vg0102430888	2.95E-06	2.95E-06	mr1487_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