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Detailed information for vg0413034382:

Variant ID: vg0413034382 (JBrowse)	Variation Type: SNP
Chromosome: chr04	Position: 13034382
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.00, others allele: 0.00, population size: 120. )

Flanking Sequence (100 bp) in Reference Genome:

CATAACCCTTGGTGAGTTAGCCCCTAGCTCTGCTGGGGTCATTGCCTTATCGCCATAAAGAAGCATAAATGGGCTAAACTTGGTTGGTCTTGTGGGGGTT[G/A]
TCCGAAGGGCCCAAAGAACCGATAACAATTCTTCTGGCCATTTGCCTTTCGCCGCCCCCTCAAGTCTTTTCTTTAGTGCTTCTAGGATCTTGCCATTTGC

Reverse complement sequence

GCAAATGGCAAGATCCTAGAAGCACTAAAGAAAAGACTTGAGGGGGCGGCGAAAGGCAAATGGCCAGAAGAATTGTTATCGGTTCTTTGGGCCCTTCGGA[C/T]
AACCCCCACAAGACCAACCAAGTTTAGCCCATTTATGCTTCTTTATGGCGATAAGGCAATGACCCCAGCAGAGCTAGGGGCTAACTCACCAAGGGTTATG

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	80.90%	11.30%	4.06%	3.75%	NA
All Indica	2759	76.80%	19.20%	2.61%	1.45%	NA
All Japonica	1512	96.60%	0.00%	2.98%	0.40%	NA
Aus	269	27.10%	0.40%	25.65%	46.84%	NA
Indica I	595	56.30%	41.80%	1.85%	0.00%	NA
Indica II	465	78.50%	17.40%	2.80%	1.29%	NA
Indica III	913	84.40%	10.10%	3.72%	1.75%	NA
Indica Intermediate	786	82.30%	13.60%	1.78%	2.29%	NA
Temperate Japonica	767	97.30%	0.00%	2.22%	0.52%	NA
Tropical Japonica	504	99.60%	0.00%	0.20%	0.20%	NA
Japonica Intermediate	241	88.40%	0.00%	11.20%	0.41%	NA
VI/Aromatic	96	90.60%	0.00%	4.17%	5.21%	NA
Intermediate	90	95.60%	2.20%	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
vg0413034382	G -> DEL	LOC_Os04g22970.1	N	frameshift_variant	Average:38.831; most accessible tissue: Minghui63 flag leaf, score: 76.807	N	N	N	N
vg0413034382	G -> A	LOC_Os04g22970.1	missense_variant ; p.Thr457Ile; MODERATE	nonsynonymous_codon ; T457M	Average:38.831; most accessible tissue: Minghui63 flag leaf, score: 76.807	benign	1.152	DELETERIOUS	0.04
vg0413034382	G -> A	LOC_Os04g22970.1	missense_variant ; p.Thr457Ile; MODERATE	nonsynonymous_codon ; T457I	Average:38.831; most accessible tissue: Minghui63 flag leaf, score: 76.807	possibly damaging	1.93	DELETERIOUS	0.00

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0413034382	9.60E-07	9.60E-07	mr1300	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