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Detailed information for vg1126612499:

Variant ID: vg1126612499 (JBrowse)	Variation Type: SNP
Chromosome: chr11	Position: 26612499
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.50, C: 0.50, others allele: 0.00, population size: 88. )

Flanking Sequence (100 bp) in Reference Genome:

GCTGAGCAAGCTCGGCGAGGACCCGGAGAGGGACCGCAGGGACCGGGAGGCCACGCTGATCATGCTCACACTCCTCCTCGCGCTGGCGATGCCGATCCTC[C/T]
TCTGGCTCTCCGCCGGCGAGGCGCCGGCGCCGCTCCTCGTGTGGAGGCTCTCCCTCCTCCTCTCCACCTACTTCTTCCTCTGCGCCAACGTCCTCTTCGT

Reverse complement sequence

ACGAAGAGGACGTTGGCGCAGAGGAAGAAGTAGGTGGAGAGGAGGAGGGAGAGCCTCCACACGAGGAGCGGCGCCGGCGCCTCGCCGGCGGAGAGCCAGA[G/A]
GAGGATCGGCATCGCCAGCGCGAGGAGGAGTGTGAGCATGATCAGCGTGGCCTCCCGGTCCCTGCGGTCCCTCTCCGGGTCCTCGCCGAGCTTGCTCAGC

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	41.60%	27.00%	0.51%	30.94%	NA
All Indica	2759	38.10%	39.60%	0.65%	21.64%	NA
All Japonica	1512	54.00%	2.90%	0.13%	42.92%	NA
Aus	269	14.90%	37.90%	0.37%	46.84%	NA
Indica I	595	11.80%	80.00%	0.34%	7.90%	NA
Indica II	465	26.20%	21.10%	0.65%	52.04%	NA
Indica III	913	53.60%	32.30%	0.55%	13.58%	NA
Indica Intermediate	786	47.20%	28.40%	1.02%	23.41%	NA
Temperate Japonica	767	78.10%	3.50%	0.00%	18.38%	NA
Tropical Japonica	504	24.20%	1.60%	0.00%	74.21%	NA
Japonica Intermediate	241	39.80%	3.70%	0.83%	55.60%	NA
VI/Aromatic	96	17.70%	10.40%	3.12%	68.75%	NA
Intermediate	90	43.30%	30.00%	0.00%	26.67%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1126612499	C -> T	LOC_Os11g44030.1	missense_variant ; p.Leu79Phe; MODERATE	nonsynonymous_codon ; L79F	Average:69.644; most accessible tissue: Zhenshan97 young leaf, score: 90.815	unknown	unknown	TOLERATED	0.07
vg1126612499	C -> DEL	LOC_Os11g44030.1	N	frameshift_variant	Average:69.644; most accessible tissue: Zhenshan97 young leaf, score: 90.815	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1126612499	NA	1.96E-10	mr1133	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
vg1126612499	9.26E-08	2.00E-14	mr1662	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
vg1126612499	NA	7.83E-09	mr1662	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
vg1126612499	NA	7.05E-07	mr1667	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
vg1126612499	NA	7.25E-06	mr1870	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
vg1126612499	NA	4.90E-08	mr1133_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
vg1126612499	NA	2.99E-09	mr1662_2	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
vg1126612499	NA	4.71E-08	mr1662_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
vg1126612499	NA	8.85E-06	mr1667_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