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Detailed information for vg0405072995:

Variant ID: vg0405072995 (JBrowse)	Variation Type: SNP
Chromosome: chr04	Position: 5072995
Reference Allele: G	Alternative Allele: T
Primary Allele: T	Secondary Allele: G

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.74, T: 0.26, others allele: 0.00, population size: 213. )

Flanking Sequence (100 bp) in Reference Genome:

TTGATAACTGGAAGTATGTTGGAAACCCACTCAGCATATCGGTAAGGACGAATAAAACCAGCATCATACAAACGTTTAACCTCAGCCTTAATAGGTTCGA[G/T]
CATATCGGCTTTGCATCTTCTCGGCGGCTGTTGGTACGGTCTAACCCCCGGTTTGATAGGTAGCCGATGTTCAACAATGGATCGGCTGAGTCCTGGCATC

Reverse complement sequence

GATGCCAGGACTCAGCCGATCCATTGTTGAACATCGGCTACCTATCAAACCGGGGGTTAGACCGTACCAACAGCCGCCGAGAAGATGCAAAGCCGATATG[C/A]
TCGAACCTATTAAGGCTGAGGTTAAACGTTTGTATGATGCTGGTTTTATTCGTCCTTACCGATATGCTGAGTGGGTTTCCAACATACTTCCAGTTATCAA

Allele Frequencies:

Populations	Population Size	Frequency of T(primary allele)	Frequency of G(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	63.90%	33.70%	0.25%	2.05%	NA
All Indica	2759	91.30%	7.00%	0.40%	1.38%	NA
All Japonica	1512	6.90%	89.40%	0.00%	3.70%	NA
Aus	269	95.20%	4.50%	0.00%	0.37%	NA
Indica I	595	95.00%	4.20%	0.50%	0.34%	NA
Indica II	465	84.30%	9.90%	0.43%	5.38%	NA
Indica III	913	94.10%	5.70%	0.22%	0.00%	NA
Indica Intermediate	786	89.30%	8.80%	0.51%	1.40%	NA
Temperate Japonica	767	1.20%	98.70%	0.00%	0.13%	NA
Tropical Japonica	504	15.70%	73.40%	0.00%	10.91%	NA
Japonica Intermediate	241	7.10%	92.90%	0.00%	0.00%	NA
VI/Aromatic	96	91.70%	8.30%	0.00%	0.00%	NA
Intermediate	90	61.10%	35.60%	1.11%	2.22%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0405072995	G -> DEL	LOC_Os04g09470.1	N	frameshift_variant	Average:23.163; most accessible tissue: Zhenshan97 root, score: 51.776	N	N	N	N
vg0405072995	G -> T	LOC_Os04g09470.1	missense_variant ; p.Leu572Ile; MODERATE	nonsynonymous_codon ; L572I	Average:23.163; most accessible tissue: Zhenshan97 root, score: 51.776	benign	0.629	DELETERIOUS	0.02

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0405072995	NA	2.22E-16	mr1035	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
vg0405072995	NA	2.19E-06	mr1035	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
vg0405072995	NA	1.40E-42	mr1136	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
vg0405072995	NA	5.23E-13	mr1626	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
vg0405072995	6.56E-06	2.12E-29	mr1631	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
vg0405072995	5.84E-07	NA	mr1033_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
vg0405072995	NA	2.38E-15	mr1035_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
vg0405072995	NA	2.85E-06	mr1274_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
vg0405072995	NA	1.85E-62	mr1402_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
vg0405072995	NA	8.04E-06	mr1613_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
vg0405072995	NA	2.69E-32	mr1631_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
vg0405072995	NA	1.63E-07	mr1837_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
vg0405072995	NA	2.87E-18	mr1945_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
vg0405072995	NA	5.79E-06	mr1962_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