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Detailed information for vg0114542149:

Variant ID: vg0114542149 (JBrowse)	Variation Type: SNP
Chromosome: chr01	Position: 14542149
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.91, A: 0.09, others allele: 0.00, population size: 97. )

Flanking Sequence (100 bp) in Reference Genome:

GCAATGTTCAATTGGCGCCCGCCGCCGTATTGAACCCTATAATCAAACCATGGCCGTTCCGAGGATGGGCTTTGGATTTCATTGGTCAAATTTATCCTTC[G/A]
TCATCAAAGGGGCATAGGTTCGTGTTAGTTGCTACGGATTACTTCACCAAGTGGGCCGAAGCCGTACCTTTGAAGAATATGACTCATACGGAGGTAATTG

Reverse complement sequence

CAATTACCTCCGTATGAGTCATATTCTTCAAAGGTACGGCTTCGGCCCACTTGGTGAAGTAATCCGTAGCAACTAACACGAACCTATGCCCCTTTGATGA[C/T]
GAAGGATAAATTTGACCAATGAAATCCAAAGCCCATCCTCGGAACGGCCATGGTTTGATTATAGGGTTCAATACGGCGGCGGGCGCCAATTGAACATTGC

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	57.00%	16.70%	7.24%	19.09%	NA
All Indica	2759	52.40%	27.50%	7.65%	12.43%	NA
All Japonica	1512	59.90%	0.30%	4.37%	35.52%	NA
Aus	269	82.50%	2.20%	15.24%	0.00%	NA
Indica I	595	44.90%	6.20%	17.48%	31.43%	NA
Indica II	465	32.90%	43.70%	9.46%	13.98%	NA
Indica III	913	64.80%	32.50%	1.53%	1.10%	NA
Indica Intermediate	786	55.20%	28.20%	6.23%	10.31%	NA
Temperate Japonica	767	85.90%	0.30%	1.04%	12.78%	NA
Tropical Japonica	504	25.20%	0.40%	9.72%	64.68%	NA
Japonica Intermediate	241	49.40%	0.00%	3.73%	46.89%	NA
VI/Aromatic	96	66.70%	4.20%	19.79%	9.38%	NA
Intermediate	90	61.10%	18.90%	5.56%	14.44%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0114542149	G -> A	LOC_Os01g25650.1	synonymous_variant ; p.Ser1422Ser; LOW	synonymous_codon	Average:18.308; most accessible tissue: Zhenshan97 panicle, score: 28.447	N	N	N	N
vg0114542149	G -> DEL	LOC_Os01g25650.1	N	frameshift_variant	Average:18.308; most accessible tissue: Zhenshan97 panicle, score: 28.447	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0114542149	1.61E-07	1.61E-07	mr1562	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