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Detailed information for vg1126973835:

Variant ID: vg1126973835 (JBrowse)	Variation Type: SNP
Chromosome: chr11	Position: 26973835
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.89, A: 0.11, others allele: 0.00, population size: 218. )

Flanking Sequence (100 bp) in Reference Genome:

TGGAGGATTTGTTTATTTTTCTCTATTTTCTTCCTTTAGGTAATTTGTCTGTTCTGTGCTTGTTAAGGTACGCAAAGAGAATATTATTTCCCAGGAAAAG[G/A]
TGCTCCAAGCATTTGATAATGCCCTTCAGAAGCATCTTAATCCAATTCATCGGTAAGATATGTCAATCAAAGCTAGGGTGATTTTTAGAACAATTATGAT

Reverse complement sequence

ATCATAATTGTTCTAAAAATCACCCTAGCTTTGATTGACATATCTTACCGATGAATTGGATTAAGATGCTTCTGAAGGGCATTATCAAATGCTTGGAGCA[C/T]
CTTTTCCTGGGAAATAATATTCTCTTTGCGTACCTTAACAAGCACAGAACAGACAAATTACCTAAAGGAAGAAAATAGAGAAAAATAAACAAATCCTCCA

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	56.80%	41.40%	0.44%	1.38%	NA
All Indica	2759	67.00%	30.10%	0.69%	2.21%	NA
All Japonica	1512	44.40%	55.40%	0.13%	0.07%	NA
Aus	269	32.70%	67.30%	0.00%	0.00%	NA
Indica I	595	59.80%	39.00%	0.67%	0.50%	NA
Indica II	465	75.30%	24.10%	0.22%	0.43%	NA
Indica III	913	62.00%	33.10%	0.77%	4.16%	NA
Indica Intermediate	786	73.30%	23.50%	0.89%	2.29%	NA
Temperate Japonica	767	56.10%	43.50%	0.26%	0.13%	NA
Tropical Japonica	504	33.50%	66.50%	0.00%	0.00%	NA
Japonica Intermediate	241	30.30%	69.70%	0.00%	0.00%	NA
VI/Aromatic	96	31.20%	68.80%	0.00%	0.00%	NA
Intermediate	90	50.00%	46.70%	0.00%	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
vg1126973835	G -> A	LOC_Os11g44600.1	missense_variant ; p.Val90Met; MODERATE	nonsynonymous_codon ; V90M	Average:35.515; most accessible tissue: Minghui63 root, score: 55.188	benign	0.53	TOLERATED	0.07
vg1126973835	G -> DEL	LOC_Os11g44600.1	N	frameshift_variant	Average:35.515; most accessible tissue: Minghui63 root, score: 55.188	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1126973835	9.45E-07	NA	mr1276	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
vg1126973835	NA	2.05E-07	mr1191_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