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Detailed information for vg1009451893:

Variant ID: vg1009451893 (JBrowse)	Variation Type: SNP
Chromosome: chr10	Position: 9451893
Reference Allele: G	Alternative Allele: A
Primary Allele: A	Secondary Allele: G

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.82, A: 0.18, others allele: 0.00, population size: 54. )

Flanking Sequence (100 bp) in Reference Genome:

TCCCATTGACGTAGCCGTTTATATACAATGGTTTAAGATGTCGATTCTCTGTCCCCTCGGGTTTCTCGAATACTGCCTGTTCTGGTGACAGGACTAACTT[G/A]
GCCGATTCCTCTTCCACTTCATCGACATCGGCCTGATCGATCCCGAATTCAGCTGGCAATGTAAAGACCATGTTAATTGGTGCCGCTATAACACTTTTCC

Reverse complement sequence

GGAAAAGTGTTATAGCGGCACCAATTAACATGGTCTTTACATTGCCAGCTGAATTCGGGATCGATCAGGCCGATGTCGATGAAGTGGAAGAGGAATCGGC[C/T]
AAGTTAGTCCTGTCACCAGAACAGGCAGTATTCGAGAAACCCGAGGGGACAGAGAATCGACATCTTAAACCATTGTATATAAACGGCTACGTCAATGGGA

Allele Frequencies:

Populations	Population Size	Frequency of A(primary allele)	Frequency of G(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	37.60%	13.10%	2.43%	46.93%	NA
All Indica	2759	33.20%	1.40%	1.34%	64.04%	NA
All Japonica	1512	34.30%	37.10%	2.98%	25.60%	NA
Aus	269	95.90%	0.40%	1.49%	2.23%	NA
Indica I	595	68.20%	1.30%	1.01%	29.41%	NA
Indica II	465	17.60%	1.50%	1.08%	79.78%	NA
Indica III	913	18.10%	0.90%	0.99%	80.07%	NA
Indica Intermediate	786	33.60%	1.90%	2.16%	62.34%	NA
Temperate Japonica	767	26.90%	55.40%	2.22%	15.51%	NA
Tropical Japonica	504	53.80%	10.30%	2.58%	33.33%	NA
Japonica Intermediate	241	17.40%	34.90%	6.22%	41.49%	NA
VI/Aromatic	96	44.80%	0.00%	26.04%	29.17%	NA
Intermediate	90	43.30%	18.90%	4.44%	33.33%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1009451893	G -> A	LOC_Os10g18640.1	synonymous_variant ; p.Ala69Ala; LOW	synonymous_codon	Average:25.89; most accessible tissue: Zhenshan97 flag leaf, score: 46.427	N	N	N	N
vg1009451893	G -> DEL	LOC_Os10g18640.1	N	frameshift_variant	Average:25.89; most accessible tissue: Zhenshan97 flag leaf, score: 46.427	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1009451893	8.32E-08	3.36E-09	mr1588_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