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Detailed information for vg0908235271:

Variant ID: vg0908235271 (JBrowse)	Variation Type: SNP
Chromosome: chr09	Position: 8235271
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.02, others allele: 0.00, population size: 59. )

Flanking Sequence (100 bp) in Reference Genome:

CGATCAGGCTATCATCAGTTGAGAATTCAGGAGGAGGATATTCCCAAGACAGCCTTCACCACTCGGTATGGGTTGTTTGAGTGCACGGTTATGTCATTTG[G/A]
ACTCACCAATGCACCGGTTTTCTTCATGAACTTGATGAACAAAGTGTTTATGGAATTTCTGGACAAGTTTGTCGTGGTGTTCATTGACGACATACTTATT

Reverse complement sequence

AATAAGTATGTCGTCAATGAACACCACGACAAACTTGTCCAGAAATTCCATAAACACTTTGTTCATCAAGTTCATGAAGAAAACCGGTGCATTGGTGAGT[C/T]
CAAATGACATAACCGTGCACTCAAACAACCCATACCGAGTGGTGAAGGCTGTCTTGGGAATATCCTCCTCCTGAATTCTCAACTGATGATAGCCTGATCG

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	92.50%	0.90%	5.04%	1.59%	NA
All Indica	2759	93.30%	1.60%	5.18%	0.00%	NA
All Japonica	1512	88.90%	0.00%	6.15%	4.96%	NA
Aus	269	100.00%	0.00%	0.00%	0.00%	NA
Indica I	595	89.20%	3.00%	7.73%	0.00%	NA
Indica II	465	94.60%	1.10%	4.30%	0.00%	NA
Indica III	913	96.90%	0.10%	2.96%	0.00%	NA
Indica Intermediate	786	91.20%	2.40%	6.36%	0.00%	NA
Temperate Japonica	767	96.30%	0.00%	1.43%	2.22%	NA
Tropical Japonica	504	84.70%	0.00%	12.30%	2.98%	NA
Japonica Intermediate	241	73.90%	0.00%	8.30%	17.84%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	97.80%	0.00%	2.22%	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
vg0908235271	G -> DEL	LOC_Os09g13980.1	N	frameshift_variant	Average:23.874; most accessible tissue: Minghui63 young leaf, score: 61.007	N	N	N	N
vg0908235271	G -> A	LOC_Os09g13980.1	missense_variant ; p.Gly224Glu; MODERATE	nonsynonymous_codon ; G224E	Average:23.874; most accessible tissue: Minghui63 young leaf, score: 61.007	benign	0.908	DELETERIOUS	0.00

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0908235271	NA	2.46E-07	mr1089	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
vg0908235271	NA	8.91E-13	mr1109	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
vg0908235271	NA	9.91E-10	mr1129	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
vg0908235271	3.77E-07	NA	mr1251	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
vg0908235271	6.55E-07	6.31E-11	mr1251	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
vg0908235271	NA	6.29E-07	mr1253	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
vg0908235271	NA	7.30E-18	mr1255	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
vg0908235271	NA	1.52E-08	mr1255	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
vg0908235271	NA	3.51E-09	mr1257	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
vg0908235271	NA	9.69E-07	mr1423	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
vg0908235271	NA	1.59E-08	mr1435	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
vg0908235271	NA	1.18E-06	mr1599	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
vg0908235271	NA	2.65E-12	mr1109_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
vg0908235271	NA	2.45E-10	mr1129_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
vg0908235271	NA	2.36E-08	mr1236_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
vg0908235271	NA	2.61E-08	mr1236_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
vg0908235271	NA	5.36E-07	mr1255_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
vg0908235271	NA	1.18E-09	mr1257_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
vg0908235271	NA	2.15E-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