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Detailed information for vg1126641326:

Variant ID: vg1126641326 (JBrowse)	Variation Type: SNP
Chromosome: chr11	Position: 26641326
Reference Allele: C	Alternative Allele: G
Primary Allele: G	Secondary Allele: C

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.77, G: 0.23, others allele: 0.00, population size: 30. )

Flanking Sequence (100 bp) in Reference Genome:

AGGAAAACAGTCAAGGCAAGGACACCAATCCAGAAGACCACCATGGCAGCAACATCACCAAAGACGATGGAGAAAAATAGGGGCAAAGCTGCGACGACTA[C/G]
GAAGACGGCGATGATAGTGTACAAGTGGTTTTCCTCTCCGATTTGCAGCAGGAAGCAAAAGACATATAACATGACGACGATGGACAGGTCGCCGACGATC

Reverse complement sequence

GATCGTCGGCGACCTGTCCATCGTCGTCATGTTATATGTCTTTTGCTTCCTGCTGCAAATCGGAGAGGAAAACCACTTGTACACTATCATCGCCGTCTTC[G/C]
TAGTCGTCGCAGCTTTGCCCCTATTTTTCTCCATCGTCTTTGGTGATGTTGCTGCCATGGTGGTCTTCTGGATTGGTGTCCTTGCCTTGACTGTTTTCCT

Allele Frequencies:

Populations	Population Size	Frequency of G(primary allele)	Frequency of C(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	46.70%	28.80%	0.87%	23.59%	NA
All Indica	2759	67.40%	14.90%	0.91%	16.85%	NA
All Japonica	1512	11.20%	57.10%	0.79%	30.95%	NA
Aus	269	40.50%	16.40%	0.00%	43.12%	NA
Indica I	595	69.40%	23.70%	0.67%	6.22%	NA
Indica II	465	37.40%	25.40%	0.65%	36.56%	NA
Indica III	913	86.50%	1.00%	0.99%	11.50%	NA
Indica Intermediate	786	61.30%	18.10%	1.15%	19.47%	NA
Temperate Japonica	767	10.00%	80.10%	0.26%	9.65%	NA
Tropical Japonica	504	10.30%	28.20%	0.99%	60.52%	NA
Japonica Intermediate	241	16.60%	44.40%	2.07%	36.93%	NA
VI/Aromatic	96	34.40%	13.50%	4.17%	47.92%	NA
Intermediate	90	42.20%	35.60%	0.00%	22.22%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1126641326	C -> DEL	LOC_Os11g44110.1	N	frameshift_variant	Average:55.842; most accessible tissue: Zhenshan97 young leaf, score: 81.6	N	N	N	N
vg1126641326	C -> G	LOC_Os11g44110.1	missense_variant ; p.Thr20Arg; MODERATE	nonsynonymous_codon ; T20R	Average:55.842; most accessible tissue: Zhenshan97 young leaf, score: 81.6	unknown	unknown	DELETERIOUS	0.00

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1126641326	1.52E-06	1.52E-06	mr1966	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