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Detailed information for vg1126443699:

Variant ID: vg1126443699 (JBrowse)	Variation Type: SNP
Chromosome: chr11	Position: 26443699
Reference Allele: T	Alternative Allele: C
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.68, C: 0.31, others allele: 0.00, population size: 191. )

Flanking Sequence (100 bp) in Reference Genome:

CTCAAGTATTTGAGCCTCCGGAACACGGGCGTCACCCAGCTGCCCAAGCACATACAAAATCTCCAGCAACTTGAGACGCTGGACGTCCGGGGAACCAATG[T/C]
GAGCAAGTTGGACGTGGTGCTCCCGATGCTGAAGGAGCTGCATTCTGGCCAATCGGAATGGTCCCTCTACCGCTCCCGCCGTCGCCGTGAGCGGTATGGA

Reverse complement sequence

TCCATACCGCTCACGGCGACGGCGGGAGCGGTAGAGGGACCATTCCGATTGGCCAGAATGCAGCTCCTTCAGCATCGGGAGCACCACGTCCAACTTGCTC[A/G]
CATTGGTTCCCCGGACGTCCAGCGTCTCAAGTTGCTGGAGATTTTGTATGTGCTTGGGCAGCTGGGTGACGCCCGTGTTCCGGAGGCTCAAATACTTGAG

Allele Frequencies:

Populations	Population Size	Frequency of T(primary allele)	Frequency of C(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	77.50%	22.50%	0.04%	0.00%	NA
All Indica	2759	65.80%	34.20%	0.04%	0.00%	NA
All Japonica	1512	96.20%	3.70%	0.07%	0.00%	NA
Aus	269	80.70%	19.30%	0.00%	0.00%	NA
Indica I	595	55.00%	45.00%	0.00%	0.00%	NA
Indica II	465	95.10%	4.90%	0.00%	0.00%	NA
Indica III	913	55.20%	44.80%	0.00%	0.00%	NA
Indica Intermediate	786	69.00%	30.90%	0.13%	0.00%	NA
Temperate Japonica	767	95.30%	4.60%	0.13%	0.00%	NA
Tropical Japonica	504	98.40%	1.60%	0.00%	0.00%	NA
Japonica Intermediate	241	94.60%	5.40%	0.00%	0.00%	NA
VI/Aromatic	96	97.90%	2.10%	0.00%	0.00%	NA
Intermediate	90	90.00%	10.00%	0.00%	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
vg1126443699	T -> C	LOC_Os11g43770.1	missense_variant ; p.Val103Ala; MODERATE	nonsynonymous_codon ; V103A	Average:71.421; most accessible tissue: Zhenshan97 young leaf, score: 82.077	unknown	unknown	TOLERATED	0.09

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1126443699	1.76E-07	1.76E-07	mr1191	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
vg1126443699	9.54E-07	9.54E-07	mr1644	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
vg1126443699	2.48E-07	2.48E-07	mr1191_2	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