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Detailed information for vg0517418107:

Variant ID: vg0517418107 (JBrowse)	Variation Type: SNP
Chromosome: chr05	Position: 17418107
Reference Allele: T	Alternative Allele: A
Primary Allele: A	Secondary Allele: T

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.93, A: 0.07, G: 0.00, others allele: 0.00, population size: 281. )

Flanking Sequence (100 bp) in Reference Genome:

CGTTCGGCGCTTCAACGAGTGCAGAAATACAATCCCCAAAATCACTGATGCTTCTGTAATTCGCGCCTTCAAATCCGGTGTCAGAGATCGCTACACTACC[T/A]
AGGAGTTGGCGACAAGACGCATCACAACTACTCGGAGATTGTTCGAGATTGTTGAGCGATGCGCCCATGCAGATGATGCGCTAAGACGCAAGAACGATAA

Reverse complement sequence

TTATCGTTCTTGCGTCTTAGCGCATCATCTGCATGGGCGCATCGCTCAACAATCTCGAACAATCTCCGAGTAGTTGTGATGCGTCTTGTCGCCAACTCCT[A/T]
GGTAGTGTAGCGATCTCTGACACCGGATTTGAAGGCGCGAATTACAGAAGCATCAGTGATTTTGGGGATTGTATTTCTGCACTCGTTGAAGCGCCGAACG

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	67.00%	32.60%	0.11%	0.32%	NA
All Indica	2759	98.30%	1.30%	0.07%	0.36%	NA
All Japonica	1512	12.80%	86.90%	0.20%	0.13%	NA
Aus	269	74.70%	25.30%	0.00%	0.00%	NA
Indica I	595	98.80%	0.80%	0.00%	0.34%	NA
Indica II	465	98.50%	1.10%	0.00%	0.43%	NA
Indica III	913	98.70%	1.00%	0.11%	0.22%	NA
Indica Intermediate	786	97.30%	2.00%	0.13%	0.51%	NA
Temperate Japonica	767	3.50%	96.30%	0.13%	0.00%	NA
Tropical Japonica	504	30.40%	69.20%	0.20%	0.20%	NA
Japonica Intermediate	241	5.40%	93.80%	0.41%	0.41%	NA
VI/Aromatic	96	6.20%	92.70%	0.00%	1.04%	NA
Intermediate	90	58.90%	38.90%	0.00%	2.22%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0517418107	T -> DEL	N	N	silent_mutation	Average:41.995; most accessible tissue: Minghui63 flag leaf, score: 68.16	N	N	N	N
vg0517418107	T -> A	LOC_Os05g30090.1	intron_variant ; MODIFIER	silent_mutation	Average:41.995; most accessible tissue: Minghui63 flag leaf, score: 68.16	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0517418107	2.58E-06	2.58E-06	mr1187	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
vg0517418107	NA	7.92E-06	mr1642	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
vg0517418107	NA	2.77E-08	mr1827	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
vg0517418107	NA	6.98E-06	mr1892_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