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Detailed information for vg0711410816:

Variant ID: vg0711410816 (JBrowse)	Variation Type: SNP
Chromosome: chr07	Position: 11410816
Reference Allele: C	Alternative Allele: T
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 1.00, others allele: 0.00, population size: 204. )

Flanking Sequence (100 bp) in Reference Genome:

GTTGAAATAAATAGAGAATTTAAATATAGGATCAACATGCTCAAAGGAATTGTGTTTGGGATCTGTGTGACTTGCCTTGCAATAACGGGTCTTCAATTAA[C/T]
CTTCTTGAACACTTCCGAGGCACTTACGATCCTTCGAAACGACGGAAACGACAAGCTAACACGCAAAACGAGAAAAAAGACTAATAAAAACCAAATAAAC

Reverse complement sequence

GTTTATTTGGTTTTTATTAGTCTTTTTTCTCGTTTTGCGTGTTAGCTTGTCGTTTCCGTCGTTTCGAAGGATCGTAAGTGCCTCGGAAGTGTTCAAGAAG[G/A]
TTAATTGAAGACCCGTTATTGCAAGGCAAGTCACACAGATCCCAAACACAATTCCTTTGAGCATGTTGATCCTATATTTAAATTCTCTATTTATTTCAAC

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	40.80%	27.00%	13.50%	18.71%	NA
All Indica	2759	50.00%	4.00%	15.80%	30.23%	NA
All Japonica	1512	19.80%	74.40%	5.09%	0.66%	NA
Aus	269	52.40%	3.00%	35.69%	8.92%	NA
Indica I	595	40.50%	4.70%	7.56%	47.23%	NA
Indica II	465	21.30%	6.70%	16.13%	55.91%	NA
Indica III	913	69.40%	1.00%	19.72%	9.86%	NA
Indica Intermediate	786	51.70%	5.20%	17.30%	25.83%	NA
Temperate Japonica	767	33.10%	65.30%	0.52%	1.04%	NA
Tropical Japonica	504	1.00%	85.90%	13.10%	0.00%	NA
Japonica Intermediate	241	17.00%	79.30%	2.90%	0.83%	NA
VI/Aromatic	96	84.40%	0.00%	14.58%	1.04%	NA
Intermediate	90	28.90%	37.80%	16.67%	16.67%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0711410816	C -> DEL	N	N	silent_mutation	Average:6.803; most accessible tissue: Callus, score: 11.104	N	N	N	N
vg0711410816	C -> T	LOC_Os07g19274.1	downstream_gene_variant ; 913.0bp to feature; MODIFIER	silent_mutation	Average:6.803; most accessible tissue: Callus, score: 11.104	N	N	N	N
vg0711410816	C -> T	LOC_Os07g19274-LOC_Os07g19290	intergenic_region ; MODIFIER	silent_mutation	Average:6.803; most accessible tissue: Callus, score: 11.104	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0711410816	NA	7.86E-08	Awn_length	Jap_All	Not	Breeding signatures of rice improvement revealed by a genomic variation map from a large germplasm collection, Proc Natl Acad Sci USA, 112(39): E5411-E5419, PMID:26358652
vg0711410816	NA	3.58E-06	mr1192	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
vg0711410816	NA	1.61E-08	mr1677	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
vg0711410816	NA	3.66E-06	mr1167_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
vg0711410816	NA	1.15E-06	mr1269_2	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
vg0711410816	NA	2.07E-06	mr1289_2	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
vg0711410816	NA	1.89E-06	mr1405_2	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
vg0711410816	NA	1.47E-06	mr1418_2	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
vg0711410816	NA	6.49E-10	mr1479_2	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
vg0711410816	NA	2.23E-06	mr1488_2	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
vg0711410816	NA	1.41E-07	mr1662_2	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
vg0711410816	NA	7.45E-16	mr1726_2	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
vg0711410816	NA	3.66E-06	mr1726_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
vg0711410816	NA	6.93E-06	mr1741_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
vg0711410816	NA	9.65E-09	mr1765_2	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