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Detailed information for vg1128469268:

Variant ID: vg1128469268 (JBrowse)	Variation Type: SNP
Chromosome: chr11	Position: 28469268
Reference Allele: T	Alternative Allele: A
Primary Allele: T	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

TCTCCATGGACAGAGCACCAACCATTTCCCAAATTATGTTTCTACATGCACATAAATAGTCTCCGGCACTTGCTAACTGCAGTTTAGCAAAATCATGAAT[T/A]
GGATTCTGGGTGCTGCGTGTGGCAATTTAAAATAGCCAGACAAACATCAAACATACATAAGCAATTTGTCCAAAAAGCGTTCATATTTGCACGGAGTTCC

Reverse complement sequence

GGAACTCCGTGCAAATATGAACGCTTTTTGGACAAATTGCTTATGTATGTTTGATGTTTGTCTGGCTATTTTAAATTGCCACACGCAGCACCCAGAATCC[A/T]
ATTCATGATTTTGCTAAACTGCAGTTAGCAAGTGCCGGAGACTATTTATGTGCATGTAGAAACATAATTTGGGAAATGGTTGGTGCTCTGTCCATGGAGA

Allele Frequencies:

Populations	Population Size	Frequency of T(primary allele)	Frequency of A(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	66.20%	12.30%	1.08%	20.46%	NA
All Indica	2759	75.90%	2.60%	0.94%	20.55%	NA
All Japonica	1512	52.60%	28.90%	1.32%	17.20%	NA
Aus	269	59.10%	20.80%	0.74%	19.33%	NA
Indica I	595	73.40%	3.70%	0.84%	22.02%	NA
Indica II	465	76.60%	1.90%	3.01%	18.49%	NA
Indica III	913	74.50%	2.10%	0.33%	23.11%	NA
Indica Intermediate	786	79.10%	2.70%	0.51%	17.68%	NA
Temperate Japonica	767	62.60%	22.90%	2.22%	12.26%	NA
Tropical Japonica	504	40.30%	34.30%	0.20%	25.20%	NA
Japonica Intermediate	241	46.50%	36.50%	0.83%	16.18%	NA
VI/Aromatic	96	27.10%	2.10%	2.08%	68.75%	NA
Intermediate	90	58.90%	15.60%	1.11%	24.44%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1128469268	T -> A	LOC_Os11g47320.1	intron_variant ; MODIFIER	silent_mutation	Average:37.811; most accessible tissue: Zhenshan97 flower, score: 79.026	N	N	N	N
vg1128469268	T -> A	LOC_Os11g47320.2	intron_variant ; MODIFIER	silent_mutation	Average:37.811; most accessible tissue: Zhenshan97 flower, score: 79.026	N	N	N	N
vg1128469268	T -> DEL	N	N	silent_mutation	Average:37.811; most accessible tissue: Zhenshan97 flower, score: 79.026	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1128469268	3.77E-06	2.24E-06	mr1126	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