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Detailed information for vg1123957709:

Variant ID: vg1123957709 (JBrowse)	Variation Type: SNP
Chromosome: chr11	Position: 23957709
Reference Allele: C	Alternative Allele: T
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.97, T: 0.02, others allele: 0.00, population size: 38. )

Flanking Sequence (100 bp) in Reference Genome:

ATATATTTTGAAATTTAATTTTAAAATTACATTTTGGGACAAAAAATGACTTAAAATAAAAAAATATCAACTATAAAGTTGTAGATCGCGTCGAGGGCTA[C/T]
AAGTTTGATATAAAGTTTTTCTTCATTAGAATTCACATGAAAAAGTTATGAATTATTTTTAAATATAAAGTCTTTAGACTGTCTTATTTGACCCAGATGA

Reverse complement sequence

TCATCTGGGTCAAATAAGACAGTCTAAAGACTTTATATTTAAAAATAATTCATAACTTTTTCATGTGAATTCTAATGAAGAAAAACTTTATATCAAACTT[G/A]
TAGCCCTCGACGCGATCTACAACTTTATAGTTGATATTTTTTTATTTTAAGTCATTTTTTGTCCCAAAATGTAATTTTAAAATTAAATTTCAAAATATAT

Allele Frequencies:

Populations	Population Size	Frequency of T(primary allele)	Frequency of C(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	33.30%	22.30%	4.04%	40.29%	NA
All Indica	2759	48.10%	9.60%	5.62%	36.75%	NA
All Japonica	1512	12.10%	41.20%	1.06%	45.63%	NA
Aus	269	14.90%	34.20%	4.46%	46.47%	NA
Indica I	595	69.60%	3.00%	1.68%	25.71%	NA
Indica II	465	44.10%	8.00%	6.67%	41.29%	NA
Indica III	913	40.00%	13.00%	6.90%	40.09%	NA
Indica Intermediate	786	43.50%	11.50%	6.49%	38.55%	NA
Temperate Japonica	767	3.00%	50.70%	1.56%	44.72%	NA
Tropical Japonica	504	15.90%	37.50%	0.40%	46.23%	NA
Japonica Intermediate	241	33.20%	18.70%	0.83%	47.30%	NA
VI/Aromatic	96	9.40%	50.00%	2.08%	38.54%	NA
Intermediate	90	18.90%	32.20%	6.67%	42.22%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1123957709	C -> T	LOC_Os11g40170.1	upstream_gene_variant ; 4550.0bp to feature; MODIFIER	silent_mutation	Average:13.669; most accessible tissue: Zhenshan97 root, score: 27.411	N	N	N	N
vg1123957709	C -> T	LOC_Os11g40170-LOC_Os11g40180	intergenic_region ; MODIFIER	silent_mutation	Average:13.669; most accessible tissue: Zhenshan97 root, score: 27.411	N	N	N	N
vg1123957709	C -> DEL	N	N	silent_mutation	Average:13.669; most accessible tissue: Zhenshan97 root, score: 27.411	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1123957709	2.63E-06	NA	mr1587_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