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Detailed information for vg0124212768:

Variant ID: vg0124212768 (JBrowse)	Variation Type: SNP
Chromosome: chr01	Position: 24212768
Reference Allele: G	Alternative Allele: A
Primary Allele: A	Secondary Allele: G

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.98, A: 0.03, others allele: 0.00, population size: 236. )

Flanking Sequence (100 bp) in Reference Genome:

GTCAATTGGATGATCCTTGGAAAGAGCGGTGTGTATCCTTAGTGGCATAGGTGGATCTTGTGCCTTCTCCTCCTCCACTTCAACTTGAGCTTGACTTGGC[G/A]
TAGCGGAAGTAGATGGCTCATCTTGAGTGGAGGTGGATGGCTTGTCTTCCACTTCAATAGGCTTGACATTTCCAATAGACATGTTCTTCATAGCTCTCAT

Reverse complement sequence

ATGAGAGCTATGAAGAACATGTCTATTGGAAATGTCAAGCCTATTGAAGTGGAAGACAAGCCATCCACCTCCACTCAAGATGAGCCATCTACTTCCGCTA[C/T]
GCCAAGTCAAGCTCAAGTTGAAGTGGAGGAGGAGAAGGCACAAGATCCACCTATGCCACTAAGGATACACACCGCTCTTTCCAAGGATCATCCAATTGAC

Allele Frequencies:

Populations	Population Size	Frequency of A(primary allele)	Frequency of G(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	50.80%	48.80%	0.21%	0.13%	NA
All Indica	2759	85.50%	14.10%	0.22%	0.14%	NA
All Japonica	1512	0.50%	99.30%	0.07%	0.07%	NA
Aus	269	0.00%	100.00%	0.00%	0.00%	NA
Indica I	595	88.90%	10.80%	0.17%	0.17%	NA
Indica II	465	95.50%	4.30%	0.00%	0.22%	NA
Indica III	913	83.70%	16.00%	0.22%	0.11%	NA
Indica Intermediate	786	79.30%	20.20%	0.38%	0.13%	NA
Temperate Japonica	767	0.10%	99.90%	0.00%	0.00%	NA
Tropical Japonica	504	0.80%	99.00%	0.00%	0.20%	NA
Japonica Intermediate	241	1.20%	98.30%	0.41%	0.00%	NA
VI/Aromatic	96	2.10%	97.90%	0.00%	0.00%	NA
Intermediate	90	36.70%	58.90%	3.33%	1.11%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0124212768	G -> A	LOC_Os01g42590.1	missense_variant ; p.Thr380Met; MODERATE	nonsynonymous_codon ; T380M	Average:31.303; most accessible tissue: Minghui63 panicle, score: 46.754	probably damaging	2.408	TOLERATED	0.16
vg0124212768	G -> DEL	LOC_Os01g42590.1	N	frameshift_variant	Average:31.303; most accessible tissue: Minghui63 panicle, score: 46.754	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0124212768	NA	2.81E-32	mr1026	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
vg0124212768	NA	5.85E-07	mr1220	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
vg0124212768	NA	3.48E-15	mr1261	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
vg0124212768	NA	2.28E-11	mr1609	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
vg0124212768	NA	1.36E-16	mr1870	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
vg0124212768	NA	4.39E-13	mr1883	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
vg0124212768	NA	5.28E-50	mr1063_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
vg0124212768	NA	9.82E-07	mr1346_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
vg0124212768	NA	8.67E-24	mr1422_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
vg0124212768	4.32E-06	NA	mr1792_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
vg0124212768	NA	2.12E-06	mr1792_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
vg0124212768	NA	2.40E-06	mr1803_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
vg0124212768	NA	6.25E-07	mr1834_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
vg0124212768	NA	3.84E-20	mr1870_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
vg0124212768	NA	3.91E-29	mr1932_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