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Detailed information for vg1207251878:

Variant ID: vg1207251878 (JBrowse)	Variation Type: SNP
Chromosome: chr12	Position: 7251878
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

GGTTCCCAAAGGTAACCCCAAATAAGTGAATGGAAGAGAACCGATCTTACATCCCAAAATGCTAGATAGTAAGACAACTTTGTCCTGAGGCATATTAAGT[G/A]
GGTACAGAGTTGATTTATTATAGTTTACCTTGAGGCCTGTGGATTGAGCAAACATATTCAAAATAGCCTTGAAATAGAAGACTTCTTTCTGAGATGCTTT

Reverse complement sequence

AAAGCATCTCAGAAAGAAGTCTTCTATTTCAAGGCTATTTTGAATATGTTTGCTCAATCCACAGGCCTCAAGGTAAACTATAATAAATCAACTCTGTACC[C/T]
ACTTAATATGCCTCAGGACAAAGTTGTCTTACTATCTAGCATTTTGGGATGTAAGATCGGTTCTCTTCCATTCACTTATTTGGGGTTACCTTTGGGAACC

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	92.70%	7.30%	0.00%	0.00%	NA
All Indica	2759	87.70%	12.30%	0.00%	0.00%	NA
All Japonica	1512	99.80%	0.20%	0.00%	0.00%	NA
Aus	269	100.00%	0.00%	0.00%	0.00%	NA
Indica I	595	99.20%	0.80%	0.00%	0.00%	NA
Indica II	465	59.10%	40.90%	0.00%	0.00%	NA
Indica III	913	96.40%	3.60%	0.00%	0.00%	NA
Indica Intermediate	786	85.80%	14.20%	0.00%	0.00%	NA
Temperate Japonica	767	99.70%	0.30%	0.00%	0.00%	NA
Tropical Japonica	504	100.00%	0.00%	0.00%	0.00%	NA
Japonica Intermediate	241	99.60%	0.40%	0.00%	0.00%	NA
VI/Aromatic	96	99.00%	1.00%	0.00%	0.00%	NA
Intermediate	90	96.70%	3.30%	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
vg1207251878	G -> A	LOC_Os12g13060.1	missense_variant ; p.Pro221Leu; MODERATE	nonsynonymous_codon ; P221L	Average:34.899; most accessible tissue: Minghui63 young leaf, score: 45.896	unknown	unknown	DELETERIOUS	0.00

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1207251878	8.96E-07	2.23E-11	mr1024_2	Ind_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
vg1207251878	7.67E-06	3.74E-16	mr1565_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
vg1207251878	1.19E-06	5.55E-14	mr1565_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