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Detailed information for vg1126851649:

Variant ID: vg1126851649 (JBrowse)	Variation Type: SNP
Chromosome: chr11	Position: 26851649
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.99, T: 0.01, others allele: 0.00, population size: 72. )

Flanking Sequence (100 bp) in Reference Genome:

TCCAAAGAAGACAAGAAAAGAAAAGCAATGATCCGAATGGATCGAAAAGAACGAAACCCTAACCCTAATCCCTTACCACGTCGCCGGTCATTGTCAACGC[C/T]
AGCAAAGGGGGGAGGGCAAAGGGCACCGCCTTGGGGCCCCTCGATGGCTGTGCATGCACCCACGGGTGCACGCGCGTGCCGGCGAGGGGGCCGTGGCGGC

Reverse complement sequence

GCCGCCACGGCCCCCTCGCCGGCACGCGCGTGCACCCGTGGGTGCATGCACAGCCATCGAGGGGCCCCAAGGCGGTGCCCTTTGCCCTCCCCCCTTTGCT[G/A]
GCGTTGACAATGACCGGCGACGTGGTAAGGGATTAGGGTTAGGGTTTCGTTCTTTTCGATCCATTCGGATCATTGCTTTTCTTTTCTTGTCTTCTTTGGA

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	58.50%	13.30%	0.44%	27.78%	NA
All Indica	2759	40.30%	17.30%	0.58%	41.83%	NA
All Japonica	1512	88.70%	5.40%	0.33%	5.62%	NA
Aus	269	59.10%	19.00%	0.00%	21.93%	NA
Indica I	595	47.10%	18.50%	0.50%	33.95%	NA
Indica II	465	45.20%	10.30%	0.65%	43.87%	NA
Indica III	913	32.00%	20.30%	0.55%	47.21%	NA
Indica Intermediate	786	42.00%	17.00%	0.64%	40.33%	NA
Temperate Japonica	767	93.60%	1.60%	0.13%	4.69%	NA
Tropical Japonica	504	81.30%	13.10%	0.79%	4.76%	NA
Japonica Intermediate	241	88.40%	1.20%	0.00%	10.37%	NA
VI/Aromatic	96	88.50%	10.40%	0.00%	1.04%	NA
Intermediate	90	75.60%	8.90%	0.00%	15.56%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1126851649	C -> T	LOC_Os11g44390.1	missense_variant ; p.Gly37Ser; MODERATE	nonsynonymous_codon ; G37S	Average:67.068; most accessible tissue: Zhenshan97 young leaf, score: 87.443	unknown	unknown	DELETERIOUS	0.00
vg1126851649	C -> DEL	LOC_Os11g44390.1	N	frameshift_variant	Average:67.068; most accessible tissue: Zhenshan97 young leaf, score: 87.443	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1126851649	2.06E-06	2.06E-06	mr1191	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
vg1126851649	4.43E-06	4.43E-06	mr1644	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
vg1126851649	NA	5.38E-06	mr1553_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