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Detailed information for vg1211062870:

Variant ID: vg1211062870 (JBrowse)	Variation Type: SNP
Chromosome: chr12	Position: 11062870
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.00, others allele: 0.00, population size: 277. )

Flanking Sequence (100 bp) in Reference Genome:

GTGTTTCAATACTGTATTAATCGTAGCACATATCGTTACTTTATCAGCTAGTATGTACGATAAGAACTTAACACCAGAAGGTCTAAGATGACCGATATAT[G/A]
TAGTGTAAAACTAACTTTCAAGGTGAGTATAATGTAAAATTGTAAGTGCTCCATATAACAAGAATATGAAGGACCTGTGCAACAAAATAAATCACATTTA

Reverse complement sequence

TAAATGTGATTTATTTTGTTGCACAGGTCCTTCATATTCTTGTTATATGGAGCACTTACAATTTTACATTATACTCACCTTGAAAGTTAGTTTTACACTA[C/T]
ATATATCGGTCATCTTAGACCTTCTGGTGTTAAGTTCTTATCGTACATACTAGCTGATAAAGTAACGATATGTGCTACGATTAATACAGTATTGAAACAC

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	91.40%	6.70%	1.95%	0.00%	NA
All Indica	2759	99.60%	0.10%	0.22%	0.00%	NA
All Japonica	1512	74.60%	20.20%	5.22%	0.00%	NA
Aus	269	99.30%	0.00%	0.74%	0.00%	NA
Indica I	595	100.00%	0.00%	0.00%	0.00%	NA
Indica II	465	98.50%	0.20%	1.29%	0.00%	NA
Indica III	913	99.90%	0.10%	0.00%	0.00%	NA
Indica Intermediate	786	99.70%	0.30%	0.00%	0.00%	NA
Temperate Japonica	767	94.10%	1.40%	4.43%	0.00%	NA
Tropical Japonica	504	37.30%	55.40%	7.34%	0.00%	NA
Japonica Intermediate	241	90.50%	6.20%	3.32%	0.00%	NA
VI/Aromatic	96	99.00%	0.00%	1.04%	0.00%	NA
Intermediate	90	88.90%	6.70%	4.44%	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
vg1211062870	G -> A	LOC_Os12g19040.1	intron_variant ; MODIFIER	silent_mutation	Average:47.659; most accessible tissue: Callus, score: 64.495	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1211062870	NA	5.22E-06	mr1083	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
vg1211062870	NA	4.08E-06	mr1304	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
vg1211062870	NA	4.06E-09	mr1364	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
vg1211062870	NA	6.31E-06	mr1414	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
vg1211062870	NA	8.99E-09	mr1443	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
vg1211062870	NA	8.49E-07	mr1471	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
vg1211062870	NA	7.12E-06	mr1653	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
vg1211062870	NA	4.73E-08	mr1696	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
vg1211062870	NA	3.95E-06	mr1700	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
vg1211062870	NA	4.32E-10	mr1364_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
vg1211062870	NA	1.67E-06	mr1653_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
vg1211062870	NA	2.08E-06	mr1705_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