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Detailed information for vg0127823351:

Variant ID: vg0127823351 (JBrowse)	Variation Type: SNP
Chromosome: chr01	Position: 27823351
Reference Allele: A	Alternative Allele: C
Primary Allele: A	Secondary Allele: C

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

CCCCGTTGAATCCACATGTCTCTTGGCATCAAGGCTCCCCTGTTTAGCTATTTACTCAGCCAGGGGCGTCCCATTCCACCCATGTGGTCGCACTTGTCTT[A/C]
TGTTCAGATGAAATTCTAAGAAAACGGTCCTTAAGTGCAGGAGCGGGAAACCGTACACCTGGTACGTTCCCCGGTCCACGATTTTGGAAATTCATTTAGT

Reverse complement sequence

ACTAAATGAATTTCCAAAATCGTGGACCGGGGAACGTACCAGGTGTACGGTTTCCCGCTCCTGCACTTAAGGACCGTTTTCTTAGAATTTCATCTGAACA[T/G]
AAGACAAGTGCGACCACATGGGTGGAATGGGACGCCCCTGGCTGAGTAAATAGCTAAACAGGGGAGCCTTGATGCCAAGAGACATGTGGATTCAACGGGG

Allele Frequencies:

Populations	Population Size	Frequency of A(primary allele)	Frequency of C(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	50.00%	49.80%	0.17%	0.00%	NA
All Indica	2759	15.90%	83.80%	0.29%	0.00%	NA
All Japonica	1512	99.60%	0.40%	0.00%	0.00%	NA
Aus	269	97.40%	2.60%	0.00%	0.00%	NA
Indica I	595	18.20%	81.30%	0.50%	0.00%	NA
Indica II	465	5.40%	94.00%	0.65%	0.00%	NA
Indica III	913	22.10%	77.80%	0.11%	0.00%	NA
Indica Intermediate	786	13.10%	86.80%	0.13%	0.00%	NA
Temperate Japonica	767	99.70%	0.30%	0.00%	0.00%	NA
Tropical Japonica	504	99.60%	0.40%	0.00%	0.00%	NA
Japonica Intermediate	241	99.20%	0.80%	0.00%	0.00%	NA
VI/Aromatic	96	96.90%	3.10%	0.00%	0.00%	NA
Intermediate	90	71.10%	28.90%	0.00%	0.00%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0127823351	A -> C	LOC_Os01g48520.1	upstream_gene_variant ; 1261.0bp to feature; MODIFIER	silent_mutation	Average:22.085; most accessible tissue: Zhenshan97 panicle, score: 36.038	N	N	N	N
vg0127823351	A -> C	LOC_Os01g48525.1	upstream_gene_variant ; 3622.0bp to feature; MODIFIER	silent_mutation	Average:22.085; most accessible tissue: Zhenshan97 panicle, score: 36.038	N	N	N	N
vg0127823351	A -> C	LOC_Os01g48520-LOC_Os01g48525	intergenic_region ; MODIFIER	silent_mutation	Average:22.085; most accessible tissue: Zhenshan97 panicle, score: 36.038	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0127823351	NA	1.17E-09	mr1850	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