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Detailed information for vg1126991344:

Variant ID: vg1126991344 (JBrowse)	Variation Type: SNP
Chromosome: chr11	Position: 26991344
Reference Allele: T	Alternative Allele: C
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.92, C: 0.08, others allele: 0.00, population size: 61. )

Flanking Sequence (100 bp) in Reference Genome:

CAATAGGAAAGACTTTGTTATATATTGTGATGCATCAAGGCAAGGACTAGGAGGGGTACTGATGCAGGATGGAAAGGTTGTGGCCTATGCATCGCGACAA[T/C]
TGCGACCACACGAGGAAAATTACCCTACCCATGACCTAGAGCTAGCAGCCGTGGTTCATGCGCTAAAGATTTGGAGACACTATTTGATTGGAAACCATTG

Reverse complement sequence

CAATGGTTTCCAATCAAATAGTGTCTCCAAATCTTTAGCGCATGAACCACGGCTGCTAGCTCTAGGTCATGGGTAGGGTAATTTTCCTCGTGTGGTCGCA[A/G]
TTGTCGCGATGCATAGGCCACAACCTTTCCATCCTGCATCAGTACCCCTCCTAGTCCTTGCCTTGATGCATCACAATATATAACAAAGTCTTTCCTATTG

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	28.90%	22.50%	28.63%	20.02%	NA
All Indica	2759	43.90%	12.50%	35.99%	7.58%	NA
All Japonica	1512	1.90%	40.30%	16.87%	41.01%	NA
Aus	269	35.30%	25.70%	25.65%	13.38%	NA
Indica I	595	20.70%	13.60%	45.88%	19.83%	NA
Indica II	465	68.40%	3.20%	21.29%	7.10%	NA
Indica III	913	50.30%	12.90%	36.25%	0.55%	NA
Indica Intermediate	786	39.70%	16.70%	36.90%	6.74%	NA
Temperate Japonica	767	1.70%	54.10%	16.82%	27.38%	NA
Tropical Japonica	504	1.60%	25.20%	19.84%	53.37%	NA
Japonica Intermediate	241	2.90%	27.80%	10.79%	58.51%	NA
VI/Aromatic	96	9.40%	13.50%	11.46%	65.62%	NA
Intermediate	90	23.30%	28.90%	27.78%	20.00%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1126991344	T -> DEL	LOC_Os11g44640.1	N	frameshift_variant	Average:13.167; most accessible tissue: Minghui63 young leaf, score: 21.268	N	N	N	N
vg1126991344	T -> C	LOC_Os11g44640.1	synonymous_variant ; p.Leu204Leu; LOW	synonymous_codon	Average:13.167; most accessible tissue: Minghui63 young leaf, score: 21.268	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1126991344	1.04E-06	NA	mr1933_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