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Detailed information for vg0210930737:

Variant ID: vg0210930737 (JBrowse)	Variation Type: SNP
Chromosome: chr02	Position: 10930737
Reference Allele: A	Alternative Allele: G
Primary Allele: A	Secondary Allele: G

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

TGGACCTATTGGAGCAGTCGCAGCCGGAGGAACAGGTTATGCTTTTAATGGTACTGTGGCGAATCTGGCACACACGGAATGAAATAGTGCATGGCAAACC[A/G]
GCCCCAGGAATACTAGTGTCCAAACGTTTCATTGAAAGCTATGTCCTCTCCCTTGCTGAGATCAAGCAACACCCCCAAGCAAGTCCTGAGAAGGGGAAAC

Reverse complement sequence

GTTTCCCCTTCTCAGGACTTGCTTGGGGGTGTTGCTTGATCTCAGCAAGGGAGAGGACATAGCTTTCAATGAAACGTTTGGACACTAGTATTCCTGGGGC[T/C]
GGTTTGCCATGCACTATTTCATTCCGTGTGTGCCAGATTCGCCACAGTACCATTAAAAGCATAACCTGTTCCTCCGGCTGCGACTGCTCCAATAGGTCCA

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	91.70%	0.10%	1.33%	6.81%	NA
All Indica	2759	86.60%	0.20%	2.28%	10.98%	NA
All Japonica	1512	99.90%	0.00%	0.00%	0.07%	NA
Aus	269	95.50%	0.00%	0.00%	4.46%	NA
Indica I	595	75.50%	0.80%	4.37%	19.33%	NA
Indica II	465	95.30%	0.00%	0.43%	4.30%	NA
Indica III	913	92.70%	0.00%	0.66%	6.68%	NA
Indica Intermediate	786	82.70%	0.00%	3.69%	13.61%	NA
Temperate Japonica	767	100.00%	0.00%	0.00%	0.00%	NA
Tropical Japonica	504	99.80%	0.00%	0.00%	0.20%	NA
Japonica Intermediate	241	100.00%	0.00%	0.00%	0.00%	NA
VI/Aromatic	96	99.00%	0.00%	0.00%	1.04%	NA
Intermediate	90	94.40%	0.00%	0.00%	5.56%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0210930737	A -> G	LOC_Os02g18740.1	synonymous_variant ; p.Pro570Pro; LOW	synonymous_codon	Average:51.346; most accessible tissue: Zhenshan97 flower, score: 65.596	N	N	N	N
vg0210930737	A -> DEL	LOC_Os02g18740.1	N	frameshift_variant	Average:51.346; most accessible tissue: Zhenshan97 flower, score: 65.596	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0210930737	8.32E-06	7.75E-07	mr1115	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