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Detailed information for vg0143252334:

Variant ID: vg0143252334 (JBrowse)	Variation Type: SNP
Chromosome: chr01	Position: 43252334
Reference Allele: C	Alternative Allele: G
Primary Allele: C	Secondary Allele: G

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.01, others allele: 0.00, population size: 318. )

Flanking Sequence (100 bp) in Reference Genome:

AAAGCTTAATACTCACCTGTTTTGGCCGAAGGTTATACTCACGGAATTATAGCGCGTAAAGGCAAAAAATCATGAAACTTTTTGTCCTAATTTTAATATT[C/G]
ACAAACTTCACATGTAACAGGGCCTGAGGAATAAATTCATGCATTTAATATTCACGTGTTTTGGTCGGAGTTTATAACTCACAAAATTATAGCCTAAAAG

Reverse complement sequence

CTTTTAGGCTATAATTTTGTGAGTTATAAACTCCGACCAAAACACGTGAATATTAAATGCATGAATTTATTCCTCAGGCCCTGTTACATGTGAAGTTTGT[G/C]
AATATTAAAATTAGGACAAAAAGTTTCATGATTTTTTGCCTTTACGCGCTATAATTCCGTGAGTATAACCTTCGGCCAAAACAGGTGAGTATTAAGCTTT

Allele Frequencies:

Populations	Population Size	Frequency of C(primary allele)	Frequency of G(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	88.30%	6.80%	1.10%	3.81%	NA
All Indica	2759	93.00%	0.50%	0.69%	5.76%	NA
All Japonica	1512	76.70%	20.00%	2.18%	1.12%	NA
Aus	269	100.00%	0.00%	0.00%	0.00%	NA
Indica I	595	96.30%	0.80%	0.34%	2.52%	NA
Indica II	465	72.90%	0.60%	2.37%	24.09%	NA
Indica III	913	99.50%	0.00%	0.11%	0.44%	NA
Indica Intermediate	786	94.90%	0.90%	0.64%	3.56%	NA
Temperate Japonica	767	59.70%	36.00%	3.91%	0.39%	NA
Tropical Japonica	504	96.20%	0.80%	0.20%	2.78%	NA
Japonica Intermediate	241	89.60%	9.50%	0.83%	0.00%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	90.00%	5.60%	0.00%	4.44%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0143252334	C -> G	LOC_Os01g74670.1	upstream_gene_variant ; 1624.0bp to feature; MODIFIER	silent_mutation	Average:27.386; most accessible tissue: Zhenshan97 panicle, score: 52.263	N	N	N	N
vg0143252334	C -> G	LOC_Os01g74670-LOC_Os01g74680	intergenic_region ; MODIFIER	silent_mutation	Average:27.386; most accessible tissue: Zhenshan97 panicle, score: 52.263	N	N	N	N
vg0143252334	C -> DEL	N	N	silent_mutation	Average:27.386; most accessible tissue: Zhenshan97 panicle, score: 52.263	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0143252334	3.12E-06	3.11E-06	mr1541	Jap_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