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Detailed information for vg0128509492:

Variant ID: vg0128509492 (JBrowse)	Variation Type: SNP
Chromosome: chr01	Position: 28509492
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

CGCGTGATGGTGGCGGTGTCTAGGCCGAACCTGGGCAGCGTCGGCTGCTGCTGCTCCTGCTCCATGACCAGTGGACGATCACGCCGGCGACAGGCAATGC[G/A]
GAGGGCTCGAGGGCAGATGAAGATGGTGATGAGGAAGAAGCTTAGGGCGAACGACGCGGCCAAGGCACCGAACAACATCATGGTGCTGCAGCATCCGGAG

Reverse complement sequence

CTCCGGATGCTGCAGCACCATGATGTTGTTCGGTGCCTTGGCCGCGTCGTTCGCCCTAAGCTTCTTCCTCATCACCATCTTCATCTGCCCTCGAGCCCTC[C/T]
GCATTGCCTGTCGCCGGCGTGATCGTCCACTGGTCATGGAGCAGGAGCAGCAGCAGCCGACGCTGCCCAGGTTCGGCCTAGACACCGCCACCATCACGCG

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	25.00%	18.40%	4.46%	52.12%	NA
All Indica	2759	1.50%	22.10%	6.96%	69.48%	NA
All Japonica	1512	72.00%	16.30%	0.93%	10.78%	NA
Aus	269	3.30%	0.00%	0.74%	95.91%	NA
Indica I	595	1.80%	8.40%	6.05%	83.70%	NA
Indica II	465	3.00%	13.10%	4.95%	78.92%	NA
Indica III	913	0.40%	42.40%	9.42%	47.75%	NA
Indica Intermediate	786	1.50%	14.10%	5.98%	78.37%	NA
Temperate Japonica	767	92.70%	0.30%	0.00%	7.04%	NA
Tropical Japonica	504	32.70%	45.00%	2.78%	19.44%	NA
Japonica Intermediate	241	88.40%	7.10%	0.00%	4.56%	NA
VI/Aromatic	96	14.60%	0.00%	2.08%	83.33%	NA
Intermediate	90	31.10%	17.80%	1.11%	50.00%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0128509492	G -> A	LOC_Os01g49570.1	missense_variant ; p.Arg28Cys; MODERATE	nonsynonymous_codon ; R28C	Average:31.266; most accessible tissue: Zhenshan97 panicle, score: 49.416	unknown	unknown	DELETERIOUS	0.05
vg0128509492	G -> DEL	LOC_Os01g49570.1	N	frameshift_variant	Average:31.266; most accessible tissue: Zhenshan97 panicle, score: 49.416	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0128509492	NA	9.77E-06	mr1047	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
vg0128509492	NA	4.86E-07	mr1543	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
vg0128509492	NA	3.12E-06	mr1642	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
vg0128509492	NA	7.51E-07	mr1742	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
vg0128509492	NA	6.02E-06	mr1871	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
vg0128509492	NA	1.89E-06	mr1903	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
vg0128509492	NA	8.87E-06	mr1990	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
vg0128509492	NA	5.51E-08	mr1526_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