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Detailed information for vg1128917038:

Variant ID: vg1128917038 (JBrowse)	Variation Type: SNP
Chromosome: chr11	Position: 28917038
Reference Allele: A	Alternative Allele: G
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.90, A: 0.10, others allele: 0.00, population size: 218. )

Flanking Sequence (100 bp) in Reference Genome:

TAGTGCAGAGATGTCATATTCCATGAGATATCCAGAAAATGCAGCTACTCGTGGACCTCAAAATATTCTTGGGTTTCCTATAAAAAATGCAGACACACGC[A/G]
CAGAGAGAGACACACACAAACACATGTACACACACCCAAACACAGACACATGCATGTACACACACACATAAACGCACGTATATATGTAGATGGTGAACCG

Reverse complement sequence

CGGTTCACCATCTACATATATACGTGCGTTTATGTGTGTGTGTACATGCATGTGTCTGTGTTTGGGTGTGTGTACATGTGTTTGTGTGTGTCTCTCTCTG[T/C]
GCGTGTGTCTGCATTTTTTATAGGAAACCCAAGAATATTTTGAGGTCCACGAGTAGCTGCATTTTCTGGATATCTCATGGAATATGACATCTCTGCACTA

Allele Frequencies:

Populations	Population Size	Frequency of G(primary allele)	Frequency of A(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	54.70%	41.90%	1.44%	1.90%	NA
All Indica	2759	61.10%	33.70%	1.92%	3.23%	NA
All Japonica	1512	39.60%	59.80%	0.60%	0.00%	NA
Aus	269	73.20%	26.40%	0.37%	0.00%	NA
Indica I	595	76.60%	17.00%	3.36%	3.03%	NA
Indica II	465	57.40%	42.60%	0.00%	0.00%	NA
Indica III	913	60.80%	34.20%	0.77%	4.27%	NA
Indica Intermediate	786	52.00%	40.60%	3.31%	4.07%	NA
Temperate Japonica	767	21.60%	77.70%	0.65%	0.00%	NA
Tropical Japonica	504	72.40%	27.00%	0.60%	0.00%	NA
Japonica Intermediate	241	28.20%	71.40%	0.41%	0.00%	NA
VI/Aromatic	96	67.70%	31.20%	1.04%	0.00%	NA
Intermediate	90	42.20%	52.20%	4.44%	1.11%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1128917038	A -> DEL	LOC_Os11g47940.1	N	frameshift_variant	Average:66.611; most accessible tissue: Callus, score: 90.236	N	N	N	N
vg1128917038	A -> G	LOC_Os11g47940.1	missense_variant ; p.Thr274Ala; MODERATE	nonsynonymous_codon ; T274A	Average:66.611; most accessible tissue: Callus, score: 90.236	unknown	unknown	DELETERIOUS	0.04

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1128917038	NA	7.32E-06	mr1077	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
vg1128917038	NA	2.42E-07	mr1252	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
vg1128917038	1.22E-06	1.22E-06	mr1700	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
vg1128917038	NA	1.22E-08	mr1902	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
vg1128917038	NA	3.93E-06	mr1517_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