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Detailed information for vg0624955380:

Variant ID: vg0624955380 (JBrowse)	Variation Type: SNP
Chromosome: chr06	Position: 24955380
Reference Allele: T	Alternative Allele: A
Primary Allele: A	Secondary Allele: T

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.99, T: 0.02, others allele: 0.00, population size: 195. )

Flanking Sequence (100 bp) in Reference Genome:

TCAAGTTCTTGAGGACAGGAAAATATCTGAAGTCCAACAACGATGTTATGTTGGGGCAACCAACAATTTTCATTTCTGTTAAACTCGCAAACGCACGGTG[T/A]
AAATCAGCATACCAGCAGATAAATGGTCCTTGGTGGGATGGAAGATTGGGGCCTAGATCTCTAAGCCCATCATTCACCATGTCTGCTCCGTCAAAGCTAA

Reverse complement sequence

TTAGCTTTGACGGAGCAGACATGGTGAATGATGGGCTTAGAGATCTAGGCCCCAATCTTCCATCCCACCAAGGACCATTTATCTGCTGGTATGCTGATTT[A/T]
CACCGTGCGTTTGCGAGTTTAACAGAAATGAAAATTGTTGGTTGCCCCAACATAACATCGTTGTTGGACTTCAGATATTTTCCTGTCCTCAAGAACTTGA

Allele Frequencies:

Populations	Population Size	Frequency of A(primary allele)	Frequency of T(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	50.90%	35.80%	0.32%	13.01%	NA
All Indica	2759	74.80%	4.30%	0.51%	20.33%	NA
All Japonica	1512	5.90%	94.10%	0.00%	0.00%	NA
Aus	269	73.60%	9.30%	0.37%	16.73%	NA
Indica I	595	35.30%	0.70%	1.51%	62.52%	NA
Indica II	465	91.40%	5.60%	0.00%	3.01%	NA
Indica III	913	90.30%	1.80%	0.33%	7.67%	NA
Indica Intermediate	786	77.10%	9.30%	0.25%	13.36%	NA
Temperate Japonica	767	2.60%	97.40%	0.00%	0.00%	NA
Tropical Japonica	504	13.50%	86.50%	0.00%	0.00%	NA
Japonica Intermediate	241	0.40%	99.60%	0.00%	0.00%	NA
VI/Aromatic	96	17.70%	82.30%	0.00%	0.00%	NA
Intermediate	90	40.00%	50.00%	0.00%	10.00%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0624955380	T -> A	LOC_Os06g41670.1	3_prime_UTR_variant ; 1341.0bp to feature; MODIFIER	silent_mutation	Average:36.692; most accessible tissue: Zhenshan97 young leaf, score: 75.397	N	N	N	N
vg0624955380	T -> DEL	N	N	silent_mutation	Average:36.692; most accessible tissue: Zhenshan97 young leaf, score: 75.397	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0624955380	NA	5.83E-07	mr1559_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
vg0624955380	NA	3.02E-09	mr1600_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
vg0624955380	NA	6.79E-07	mr1668_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
vg0624955380	3.40E-06	NA	mr1723_2	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
vg0624955380	NA	9.66E-06	mr1723_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