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Detailed information for vg1217374273:

Variant ID: vg1217374273 (JBrowse)	Variation Type: SNP
Chromosome: chr12	Position: 17374273
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.99, others allele: 0.00, population size: 107. )

Flanking Sequence (100 bp) in Reference Genome:

CTCGAACTTAGCCTCTTCCTCAGGAGAAAGAGGTGGTTCACTTCGTTTGCCCCGTGAAACATAGAAGCACTGCATCGCTGTCAACCACAATAGTGCACGT[G/A]
CTTTCCATCTCTTATAATTAGGACCATCAAAAGCATGTGGTTTCAGTGCAGCAGCAAAGCCAACTACTGAAAATGACCTATCAGGTTTTTGGATTGTTGG

Reverse complement sequence

CCAACAATCCAAAAACCTGATAGGTCATTTTCAGTAGTTGGCTTTGCTGCTGCACTGAAACCACATGCTTTTGATGGTCCTAATTATAAGAGATGGAAAG[C/T]
ACGTGCACTATTGTGGTTGACAGCGATGCAGTGCTTCTATGTTTCACGGGGCAAACGAAGTGAACCACCTCTTTCTCCTGAGGAAGAGGCTAAGTTCGAG

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	59.10%	11.00%	0.25%	29.69%	NA
All Indica	2759	60.90%	0.60%	0.40%	38.17%	NA
All Japonica	1512	58.90%	30.80%	0.00%	10.32%	NA
Aus	269	59.50%	7.80%	0.00%	32.71%	NA
Indica I	595	86.20%	0.20%	0.17%	13.45%	NA
Indica II	465	74.80%	0.40%	0.86%	23.87%	NA
Indica III	913	36.50%	0.40%	0.22%	62.87%	NA
Indica Intermediate	786	61.70%	1.10%	0.51%	36.64%	NA
Temperate Japonica	767	93.50%	6.30%	0.00%	0.26%	NA
Tropical Japonica	504	13.70%	59.10%	0.00%	27.18%	NA
Japonica Intermediate	241	43.20%	49.80%	0.00%	7.05%	NA
VI/Aromatic	96	16.70%	0.00%	0.00%	83.33%	NA
Intermediate	90	53.30%	16.70%	1.11%	28.89%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1217374273	G -> DEL	LOC_Os12g29310.1	N	frameshift_variant	Average:16.326; most accessible tissue: Zhenshan97 flower, score: 32.793	N	N	N	N
vg1217374273	G -> A	LOC_Os12g29310.1	missense_variant ; p.Ala133Val; MODERATE	nonsynonymous_codon ; A133V	Average:16.326; most accessible tissue: Zhenshan97 flower, score: 32.793	benign	1.39	TOLERATED	0.13

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1217374273	4.03E-06	NA	mr1016	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
vg1217374273	2.34E-06	NA	mr1017	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
vg1217374273	2.68E-06	NA	mr1055	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
vg1217374273	3.30E-06	NA	mr1079	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
vg1217374273	NA	1.44E-06	mr1695	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
vg1217374273	3.47E-06	NA	mr1835	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
vg1217374273	4.03E-07	6.01E-07	mr1835	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
vg1217374273	1.64E-06	NA	mr1022_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
vg1217374273	4.15E-07	NA	mr1023_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
vg1217374273	1.55E-06	NA	mr1055_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
vg1217374273	2.17E-06	NA	mr1079_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
vg1217374273	NA	2.83E-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
vg1217374273	NA	3.38E-07	mr1479_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
vg1217374273	NA	1.03E-08	mr1502_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
vg1217374273	NA	2.55E-12	mr1680_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
vg1217374273	NA	2.68E-06	mr1863_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
vg1217374273	NA	1.31E-06	mr1923_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
vg1217374273	NA	1.08E-07	mr1929_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