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Detailed information for vg1128742524:

Variant ID: vg1128742524 (JBrowse)	Variation Type: SNP
Chromosome: chr11	Position: 28742524
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, others allele: 0.00, population size: 259. )

Flanking Sequence (100 bp) in Reference Genome:

ATATCAATCATATATCCCTACTAATTCCTATGTGTATAAGTTTCATATACAAATCACTATCCACCAATTATCAAGTCATATTAATTACTTATGAGGCATC[C/T]
GTGCTTAATGCACCTAATAATTAGATGACATCTAATATGCAGTGTGTTATCGAGTACTGATAATGGACAATATTAAGTGAGAAACCATCAACAAATGATA

Reverse complement sequence

TATCATTTGTTGATGGTTTCTCACTTAATATTGTCCATTATCAGTACTCGATAACACACTGCATATTAGATGTCATCTAATTATTAGGTGCATTAAGCAC[G/A]
GATGCCTCATAAGTAATTAATATGACTTGATAATTGGTGGATAGTGATTTGTATATGAAACTTATACACATAGGAATTAGTAGGGATATATGATTGATAT

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	93.80%	3.40%	1.82%	0.99%	NA
All Indica	2759	97.50%	0.30%	0.62%	1.63%	NA
All Japonica	1512	85.30%	10.10%	4.56%	0.00%	NA
Aus	269	99.30%	0.00%	0.00%	0.74%	NA
Indica I	595	99.80%	0.00%	0.17%	0.00%	NA
Indica II	465	99.10%	0.40%	0.22%	0.22%	NA
Indica III	913	94.30%	0.10%	1.20%	4.38%	NA
Indica Intermediate	786	98.50%	0.50%	0.51%	0.51%	NA
Temperate Japonica	767	76.00%	16.00%	7.95%	0.00%	NA
Tropical Japonica	504	98.20%	1.40%	0.40%	0.00%	NA
Japonica Intermediate	241	88.00%	9.50%	2.49%	0.00%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	100.00%	0.00%	0.00%	0.00%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1128742524	C -> T	LOC_Os11g47560.1	downstream_gene_variant ; 1814.0bp to feature; MODIFIER	silent_mutation	Average:25.781; most accessible tissue: Minghui63 young leaf, score: 42.042	N	N	N	N
vg1128742524	C -> T	LOC_Os11g47560-LOC_Os11g47570	intergenic_region ; MODIFIER	silent_mutation	Average:25.781; most accessible tissue: Minghui63 young leaf, score: 42.042	N	N	N	N
vg1128742524	C -> DEL	N	N	silent_mutation	Average:25.781; most accessible tissue: Minghui63 young leaf, score: 42.042	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1128742524	7.20E-07	7.20E-07	mr1972_2	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