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Detailed information for vg1117899452:

Variant ID: vg1117899452 (JBrowse)	Variation Type: SNP
Chromosome: chr11	Position: 17899452
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.01, others allele: 0.00, population size: 304. )

Flanking Sequence (100 bp) in Reference Genome:

GAATACAAGAAGGGCTTGCACAAGGAGAAATTGATTACTGTCGCACAGTACATTGGACGAGCCTTCTTACACTTTCAAAATAAGAGAGTCGTCATGGCCG[C/T]
TTATAATTTTAAGTAAGTCGGGTACATTTATCTTCTGCACATATGTCTTATTTTAGCTGGTACTAACTAACTATGCCGTTGTTAATATGTAGCGATCATT

Reverse complement sequence

AATGATCGCTACATATTAACAACGGCATAGTTAGTTAGTACCAGCTAAAATAAGACATATGTGCAGAAGATAAATGTACCCGACTTACTTAAAATTATAA[G/A]
CGGCCATGACGACTCTCTTATTTTGAAAGTGTAAGAAGGCTCGTCCAATGTACTGTGCGACAGTAATCAATTTCTCCTTGTGCAAGCCCTTCTTGTATTC

Allele Frequencies:

Populations	Population Size	Frequency of C(primary allele)	Frequency of T(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	93.80%	3.40%	2.71%	0.00%	NA
All Indica	2759	99.50%	0.10%	0.43%	0.00%	NA
All Japonica	1512	81.80%	10.60%	7.61%	0.00%	NA
Aus	269	100.00%	0.00%	0.00%	0.00%	NA
Indica I	595	98.70%	0.00%	1.34%	0.00%	NA
Indica II	465	99.80%	0.20%	0.00%	0.00%	NA
Indica III	913	99.80%	0.20%	0.00%	0.00%	NA
Indica Intermediate	786	99.50%	0.00%	0.51%	0.00%	NA
Temperate Japonica	767	70.00%	16.00%	13.95%	0.00%	NA
Tropical Japonica	504	98.60%	0.80%	0.60%	0.00%	NA
Japonica Intermediate	241	84.20%	13.70%	2.07%	0.00%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	98.90%	0.00%	1.11%	0.00%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1117899452	C -> T	LOC_Os11g30750.1	downstream_gene_variant ; 3165.0bp to feature; MODIFIER	silent_mutation	Average:34.117; most accessible tissue: Zhenshan97 root, score: 49.075	N	N	N	N
vg1117899452	C -> T	LOC_Os11g30740.1	intron_variant ; MODIFIER	silent_mutation	Average:34.117; most accessible tissue: Zhenshan97 root, score: 49.075	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1117899452	NA	1.99E-06	mr1521	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
vg1117899452	4.31E-06	4.31E-06	mr1804	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