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Detailed information for vg0111406406:

Variant ID: vg0111406406 (JBrowse)	Variation Type: SNP
Chromosome: chr01	Position: 11406406
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.99, A: 0.01, others allele: 0.00, population size: 117. )

Flanking Sequence (100 bp) in Reference Genome:

GCAGCGCTCGTAGGTTAAACTTCTCTTGTTTGTCCTCATCCCATACGGGGACACCTTCCTTCTTCCACAACAGTTTAAGATCTTCGACCAGTGGTCTTAG[G/A]
TACACATCAATGTCGTTACCAAGTTGCTTGGGGCCTTGAATTATTATCGGCATCATTATGTACTTTCTCTTCATGCATAGCTACGGGGAGAGGTTGTAGA

Reverse complement sequence

TCTACAACCTCTCCCCGTAGCTATGCATGAAGAGAAAGTACATAATGATGCCGATAATAATTCAAGGCCCCAAGCAACTTGGTAACGACATTGATGTGTA[C/T]
CTAAGACCACTGGTCGAAGATCTTAAACTGTTGTGGAAGAAGGAAGGTGTCCCCGTATGGGATGAGGACAAACAAGAGAAGTTTAACCTACGAGCGCTGC

Allele Frequencies:

Populations	Population Size	Frequency of G(primary allele)	Frequency of A(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	44.40%	2.10%	51.08%	2.41%	NA
All Indica	2759	17.70%	3.10%	75.53%	3.66%	NA
All Japonica	1512	97.20%	0.10%	2.58%	0.07%	NA
Aus	269	20.10%	3.00%	73.61%	3.35%	NA
Indica I	595	27.90%	2.90%	63.87%	5.38%	NA
Indica II	465	23.90%	2.40%	71.83%	1.94%	NA
Indica III	913	8.80%	3.90%	85.54%	1.75%	NA
Indica Intermediate	786	16.80%	2.70%	74.94%	5.60%	NA
Temperate Japonica	767	99.20%	0.00%	0.78%	0.00%	NA
Tropical Japonica	504	93.80%	0.40%	5.56%	0.20%	NA
Japonica Intermediate	241	97.90%	0.00%	2.07%	0.00%	NA
VI/Aromatic	96	39.60%	4.20%	56.25%	0.00%	NA
Intermediate	90	52.20%	1.10%	43.33%	3.33%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0111406406	G -> A	LOC_Os01g20090.1	synonymous_variant ; p.Tyr348Tyr; LOW	synonymous_codon	Average:19.072; most accessible tissue: Minghui63 young leaf, score: 26.082	N	N	N	N
vg0111406406	G -> DEL	LOC_Os01g20090.1	N	frameshift_variant	Average:19.072; most accessible tissue: Minghui63 young leaf, score: 26.082	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0111406406	3.32E-06	3.32E-06	mr1821_2	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