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Detailed information for vg1005044043:

Variant ID: vg1005044043 (JBrowse)	Variation Type: SNP
Chromosome: chr10	Position: 5044043
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.98, others allele: 0.00, population size: 68. )

Flanking Sequence (100 bp) in Reference Genome:

TGTACTAGACAGCTTCACATATTTATGATACTAATATATTGATTAACTTCAATGCATGCAGTTGCCAAGATTAGAACGTCGAACAAGCTTTGACGATACA[G/A]
ACATCACAAATGTCCAGCGTGATCTGTGCCATTTCATCCACCATGAGTGCTGTCATGTGAAAGGAGATTTCTTCGACCCAGAGGGTGCCCTAGCGACAAG

Reverse complement sequence

CTTGTCGCTAGGGCACCCTCTGGGTCGAAGAAATCTCCTTTCACATGACAGCACTCATGGTGGATGAAATGGCACAGATCACGCTGGACATTTGTGATGT[C/T]
TGTATCGTCAAAGCTTGTTCGACGTTCTAATCTTGGCAACTGCATGCATTGAAGTTAATCAATATATTAGTATCATAAATATGTGAAGCTGTCTAGTACA

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	64.10%	2.90%	0.66%	32.40%	NA
All Indica	2759	56.60%	4.90%	0.80%	37.73%	NA
All Japonica	1512	71.40%	0.00%	0.53%	28.04%	NA
Aus	269	85.10%	0.00%	0.37%	14.50%	NA
Indica I	595	49.90%	16.10%	1.51%	32.44%	NA
Indica II	465	51.00%	2.80%	0.65%	45.59%	NA
Indica III	913	62.50%	0.20%	0.66%	36.58%	NA
Indica Intermediate	786	58.10%	2.90%	0.51%	38.42%	NA
Temperate Japonica	767	80.80%	0.00%	0.13%	19.04%	NA
Tropical Japonica	504	59.30%	0.00%	0.79%	39.88%	NA
Japonica Intermediate	241	66.80%	0.00%	1.24%	31.95%	NA
VI/Aromatic	96	91.70%	0.00%	0.00%	8.33%	NA
Intermediate	90	77.80%	1.10%	0.00%	21.11%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1005044043	G -> A	LOC_Os10g09330.1	missense_variant ; p.Asp32Asn; MODERATE	nonsynonymous_codon ; D32N	Average:15.426; most accessible tissue: Callus, score: 49.421	benign	1.269	DELETERIOUS	0.03
vg1005044043	G -> DEL	LOC_Os10g09330.1	N	frameshift_variant	Average:15.426; most accessible tissue: Callus, score: 49.421	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1005044043	8.47E-07	8.38E-08	mr1519_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