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Detailed information for vg0141380906:

Variant ID: vg0141380906 (JBrowse)	Variation Type: SNP
Chromosome: chr01	Position: 41380906
Reference Allele: T	Alternative Allele: C
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.95, T: 0.04, others allele: 0.00, population size: 227. )

Flanking Sequence (100 bp) in Reference Genome:

GGGCGGATGTGAGGTGGTTCCCGTTGCGTAGATTTGTTTGCCTGTGCTTTGTGAAAAGTTGTTGTGGTGTGGGAATCGTAACCAGAATCAGCCTATGTGG[T/C]
AGATGGATGACCTGAGTGGTCAGAAACGAATCTGTGTGATTCGGGATGTCTACGGGCATCATAGACTAGGCTTCCCGAGTGGAAGCGGATTGCTTTGCTG

Reverse complement sequence

CAGCAAAGCAATCCGCTTCCACTCGGGAAGCCTAGTCTATGATGCCCGTAGACATCCCGAATCACACAGATTCGTTTCTGACCACTCAGGTCATCCATCT[A/G]
CCACATAGGCTGATTCTGGTTACGATTCCCACACCACAACAACTTTTCACAAAGCACAGGCAAACAAATCTACGCAACGGGAACCACCTCACATCCGCCC

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	55.50%	1.30%	31.17%	11.96%	NA
All Indica	2759	30.40%	2.00%	48.28%	19.32%	NA
All Japonica	1512	97.80%	0.10%	1.79%	0.33%	NA
Aus	269	87.40%	1.10%	9.67%	1.86%	NA
Indica I	595	59.00%	0.80%	32.27%	7.90%	NA
Indica II	465	15.90%	0.00%	38.92%	45.16%	NA
Indica III	913	12.90%	3.60%	69.77%	13.69%	NA
Indica Intermediate	786	37.80%	2.00%	40.97%	19.21%	NA
Temperate Japonica	767	99.30%	0.10%	0.26%	0.26%	NA
Tropical Japonica	504	96.60%	0.00%	2.78%	0.60%	NA
Japonica Intermediate	241	95.40%	0.00%	4.56%	0.00%	NA
VI/Aromatic	96	14.60%	3.10%	73.96%	8.33%	NA
Intermediate	90	63.30%	2.20%	18.89%	15.56%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0141380906	T -> DEL	N	N	silent_mutation	Average:16.683; most accessible tissue: Minghui63 young leaf, score: 21.268	N	N	N	N
vg0141380906	T -> C	LOC_Os01g71410.1	downstream_gene_variant ; 4609.0bp to feature; MODIFIER	silent_mutation	Average:16.683; most accessible tissue: Minghui63 young leaf, score: 21.268	N	N	N	N
vg0141380906	T -> C	LOC_Os01g71420.1	downstream_gene_variant ; 3380.0bp to feature; MODIFIER	silent_mutation	Average:16.683; most accessible tissue: Minghui63 young leaf, score: 21.268	N	N	N	N
vg0141380906	T -> C	LOC_Os01g71410-LOC_Os01g71420	intergenic_region ; MODIFIER	silent_mutation	Average:16.683; most accessible tissue: Minghui63 young leaf, score: 21.268	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0141380906	3.81E-06	3.81E-06	mr1753	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
vg0141380906	NA	4.05E-06	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
vg0141380906	9.38E-06	1.96E-08	mr1974	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