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Detailed information for vg0121399989:

Variant ID: vg0121399989 (JBrowse)	Variation Type: SNP
Chromosome: chr01	Position: 21399989
Reference Allele: A	Alternative Allele: G
Primary Allele: A	Secondary Allele: G

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.90, G: 0.10, others allele: 0.00, population size: 31. )

Flanking Sequence (100 bp) in Reference Genome:

GAATTTATCCGTTAACAACCTTTTCTCGAATAGCCCAGCCATGGTCGGCGCTATGAGATAGGTCGTCGGTCTTCGTTGGCAGGTTAGGTGCGATAACTCC[A/G]
CATTTGTCGAGAATGTTCTCGATAATGGGGTGTACTCGACCACAGCTTACTCGAGTGCTCAATTGTTCCTGAAAAATATTTTCTAGAAGGCAAGACATAT

Reverse complement sequence

ATATGTCTTGCCTTCTAGAAAATATTTTTCAGGAACAATTGAGCACTCGAGTAAGCTGTGGTCGAGTACACCCCATTATCGAGAACATTCTCGACAAATG[T/C]
GGAGTTATCGCACCTAACCTGCCAACGAAGACCGACGACCTATCTCATAGCGCCGACCATGGCTGGGCTATTCGAGAAAAGGTTGTTAACGGATAAATTC

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	37.20%	0.60%	0.80%	61.49%	NA
All Indica	2759	6.20%	0.90%	1.30%	91.63%	NA
All Japonica	1512	95.80%	0.00%	0.00%	4.23%	NA
Aus	269	5.90%	0.40%	0.37%	93.31%	NA
Indica I	595	5.50%	1.30%	1.01%	92.10%	NA
Indica II	465	9.00%	1.10%	1.29%	88.60%	NA
Indica III	913	3.00%	0.20%	1.53%	95.29%	NA
Indica Intermediate	786	8.70%	1.30%	1.27%	88.80%	NA
Temperate Japonica	767	95.80%	0.00%	0.00%	4.17%	NA
Tropical Japonica	504	97.60%	0.00%	0.00%	2.38%	NA
Japonica Intermediate	241	91.70%	0.00%	0.00%	8.30%	NA
VI/Aromatic	96	69.80%	0.00%	0.00%	30.21%	NA
Intermediate	90	61.10%	0.00%	1.11%	37.78%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0121399989	A -> G	LOC_Os01g38200.1	synonymous_variant ; p.Cys44Cys; LOW	synonymous_codon	Average:9.131; most accessible tissue: Callus, score: 41.331	N	N	N	N
vg0121399989	A -> DEL	LOC_Os01g38200.1	N	frameshift_variant	Average:9.131; most accessible tissue: Callus, score: 41.331	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0121399989	4.06E-06	NA	mr1308	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