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Detailed information for vg1017358348:

Variant ID: vg1017358348 (JBrowse)	Variation Type: SNP
Chromosome: chr10	Position: 17358348
Reference Allele: T	Alternative Allele: A
Primary Allele: T	Secondary Allele: A

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

Flanking Sequence (100 bp) in Reference Genome:

TTCTGAAGACTATCAATCACAAAAGTTCTGTCCTTCATCAACTTTGTATTCCTCGTTGCTACTTGCTTCTATCCCTGTGTAATATTATTATTTTTCCCAT[T/A]
GGCTAAGCAAACTTGTAAATGCAAGACAGAGAAGATAAATGAAAATCATGACATTGACATATAATTCTGTCGAGGAAAAGCAACAGGGGCATATTATTTG

Reverse complement sequence

CAAATAATATGCCCCTGTTGCTTTTCCTCGACAGAATTATATGTCAATGTCATGATTTTCATTTATCTTCTCTGTCTTGCATTTACAAGTTTGCTTAGCC[A/T]
ATGGGAAAAATAATAATATTACACAGGGATAGAAGCAAGTAGCAACGAGGAATACAAAGTTGATGAAGGACAGAACTTTTGTGATTGATAGTCTTCAGAA

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	45.30%	44.40%	0.34%	9.94%	NA
All Indica	2759	31.80%	62.30%	0.25%	5.69%	NA
All Japonica	1512	78.00%	21.20%	0.00%	0.73%	NA
Aus	269	1.10%	10.00%	2.97%	85.87%	NA
Indica I	595	19.70%	78.00%	0.34%	2.02%	NA
Indica II	465	25.80%	70.50%	0.22%	3.44%	NA
Indica III	913	41.90%	49.10%	0.22%	8.76%	NA
Indica Intermediate	786	32.70%	60.80%	0.25%	6.23%	NA
Temperate Japonica	767	97.90%	2.10%	0.00%	0.00%	NA
Tropical Japonica	504	56.70%	41.70%	0.00%	1.59%	NA
Japonica Intermediate	241	59.30%	39.40%	0.00%	1.24%	NA
VI/Aromatic	96	30.20%	6.20%	1.04%	62.50%	NA
Intermediate	90	56.70%	31.10%	0.00%	12.22%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1017358348	T -> A	LOC_Os10g33130.1	3_prime_UTR_variant ; 127.0bp to feature; MODIFIER	silent_mutation	Average:40.597; most accessible tissue: Zhenshan97 flower, score: 58.632	N	N	N	N
vg1017358348	T -> DEL	N	N	silent_mutation	Average:40.597; most accessible tissue: Zhenshan97 flower, score: 58.632	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1017358348	NA	3.35E-06	mr1124	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
vg1017358348	NA	1.24E-09	mr1191	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
vg1017358348	NA	1.46E-08	mr1644	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
vg1017358348	NA	4.67E-06	mr1704	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
vg1017358348	5.85E-07	NA	mr1952	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
vg1017358348	8.63E-06	1.76E-06	mr1952	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