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Detailed information for vg0629060911:

Variant ID: vg0629060911 (JBrowse)	Variation Type: SNP
Chromosome: chr06	Position: 29060911
Reference Allele: G	Alternative Allele: T
Primary Allele: G	Secondary Allele: T

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.99, T: 0.01, others allele: 0.00, population size: 304. )

Flanking Sequence (100 bp) in Reference Genome:

TCCTCTAGTGCTAATAGTTCCTGAGCAAATGAAAAGCAGAAGAAAATACATAACCTTCTGATGTCAGAATCAGATGAGCCGATGACACTTCTTTGTTAAG[G/T]
AAAGAGATATTCTAATTGAACCTTTGAGGAAGAATCAACATGGTGAAAGCAATACCTCATAAGACATGTTGTCAATATCCATTCTCATATCTCTGTGCTG

Reverse complement sequence

CAGCACAGAGATATGAGAATGGATATTGACAACATGTCTTATGAGGTATTGCTTTCACCATGTTGATTCTTCCTCAAAGGTTCAATTAGAATATCTCTTT[C/A]
CTTAACAAAGAAGTGTCATCGGCTCATCTGATTCTGACATCAGAAGGTTATGTATTTTCTTCTGCTTTTCATTTGCTCAGGAACTATTAGCACTAGAGGA

Allele Frequencies:

Populations	Population Size	Frequency of G(primary allele)	Frequency of T(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	75.20%	24.10%	0.08%	0.61%	NA
All Indica	2759	65.80%	33.10%	0.14%	0.94%	NA
All Japonica	1512	97.80%	2.10%	0.00%	0.13%	NA
Aus	269	69.50%	30.50%	0.00%	0.00%	NA
Indica I	595	45.20%	53.40%	0.00%	1.34%	NA
Indica II	465	61.70%	36.80%	0.43%	1.08%	NA
Indica III	913	80.30%	18.90%	0.22%	0.55%	NA
Indica Intermediate	786	67.00%	31.90%	0.00%	1.02%	NA
Temperate Japonica	767	97.90%	2.00%	0.00%	0.13%	NA
Tropical Japonica	504	97.80%	2.20%	0.00%	0.00%	NA
Japonica Intermediate	241	97.50%	2.10%	0.00%	0.41%	NA
VI/Aromatic	96	10.40%	89.60%	0.00%	0.00%	NA
Intermediate	90	66.70%	32.20%	0.00%	1.11%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0629060911	G -> T	LOC_Os06g48040.1	intron_variant ; MODIFIER	silent_mutation	Average:70.391; most accessible tissue: Minghui63 young leaf, score: 83.666	N	N	N	N
vg0629060911	G -> DEL	N	N	silent_mutation	Average:70.391; most accessible tissue: Minghui63 young leaf, score: 83.666	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0629060911	NA	9.66E-06	mr1125_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
vg0629060911	NA	6.53E-06	mr1220_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