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Detailed information for vg1213804495:

Variant ID: vg1213804495 (JBrowse)	Variation Type: SNP
Chromosome: chr12	Position: 13804495
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.92, A: 0.08, others allele: 0.00, population size: 38. )

Flanking Sequence (100 bp) in Reference Genome:

GTGGATAGCCGAGAAAGATGCACATGGTGGATCGGGGCGAGAGCTTATGTGGGGCTGTGGCGGAAAGGTTAGGATAGCACTTGCAACCGAATACGCGAAG[G/A]
TGTGCATAGGAGGGGTGTACACCATAGAGGGCAAAGAAAGGGGTGTGGTGTTGAAGCATCTTGGTGGGGTGTCTGTTGATAAGGTGGGTGGCTGTGTGAA

Reverse complement sequence

TTCACACAGCCACCCACCTTATCAACAGACACCCCACCAAGATGCTTCAACACCACACCCCTTTCTTTGCCCTCTATGGTGTACACCCCTCCTATGCACA[C/T]
CTTCGCGTATTCGGTTGCAAGTGCTATCCTAACCTTTCCGCCACAGCCCCACATAAGCTCTCGCCCCGATCCACCATGTGCATCTTTCTCGGCTATCCAC

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	16.00%	14.30%	49.20%	20.57%	NA
All Indica	2759	2.50%	16.20%	78.11%	3.12%	NA
All Japonica	1512	43.80%	0.20%	2.71%	53.31%	NA
Aus	269	0.00%	62.10%	17.10%	20.82%	NA
Indica I	595	1.30%	11.80%	80.84%	6.05%	NA
Indica II	465	3.20%	9.00%	83.87%	3.87%	NA
Indica III	913	1.50%	22.30%	75.47%	0.66%	NA
Indica Intermediate	786	4.20%	16.80%	75.70%	3.31%	NA
Temperate Japonica	767	78.50%	0.10%	1.83%	19.56%	NA
Tropical Japonica	504	0.80%	0.20%	2.98%	96.03%	NA
Japonica Intermediate	241	23.20%	0.40%	4.98%	71.37%	NA
VI/Aromatic	96	0.00%	47.90%	45.83%	6.25%	NA
Intermediate	90	24.40%	12.20%	43.33%	20.00%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1213804495	G -> DEL	LOC_Os12g24220.1	N	frameshift_variant	Average:17.436; most accessible tissue: Callus, score: 52.762	N	N	N	N
vg1213804495	G -> A	LOC_Os12g24220.1	synonymous_variant ; p.His835His; LOW	synonymous_codon	Average:17.436; most accessible tissue: Callus, score: 52.762	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1213804495	1.32E-06	NA	mr1534	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
vg1213804495	NA	3.04E-06	mr1534	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
vg1213804495	NA	1.29E-14	mr1031_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
vg1213804495	NA	1.46E-76	mr1489_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
vg1213804495	NA	5.13E-12	mr1722_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