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Detailed information for vg0100239155:

Variant ID: vg0100239155 (JBrowse)	Variation Type: SNP
Chromosome: chr01	Position: 239155
Reference Allele: C	Alternative Allele: A
Primary Allele: C	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

TTAGTCCAAGATTATGGATGGGTTTTATTAATAGTCTACGTTTAATATTTATAATTAATTTTCAAACATCCGATGTGATAGGGACTTAAAAGTTTTTAGT[C/A]
CCATCTAAACAGGACCTCAGTAGCTAGCTTTTAGTGACTACTCCTATTTAGCCCCACCTTCATTGACTTTATTAATCATATCAGCATCATATATATATAT

Reverse complement sequence

ATATATATATATGATGCTGATATGATTAATAAAGTCAATGAAGGTGGGGCTAAATAGGAGTAGTCACTAAAAGCTAGCTACTGAGGTCCTGTTTAGATGG[G/T]
ACTAAAAACTTTTAAGTCCCTATCACATCGGATGTTTGAAAATTAATTATAAATATTAAACGTAGACTATTAATAAAACCCATCCATAATCTTGGACTAA

Allele Frequencies:

Populations	Population Size	Frequency of C(primary allele)	Frequency of A(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	77.00%	0.20%	11.00%	11.85%	NA
All Indica	2759	71.70%	0.10%	16.38%	11.78%	NA
All Japonica	1512	95.40%	0.00%	3.24%	1.39%	NA
Aus	269	25.30%	1.10%	4.09%	69.52%	NA
Indica I	595	62.50%	0.50%	23.70%	13.28%	NA
Indica II	465	65.40%	0.00%	17.42%	17.20%	NA
Indica III	913	84.20%	0.00%	9.86%	5.91%	NA
Indica Intermediate	786	67.80%	0.10%	17.81%	14.25%	NA
Temperate Japonica	767	91.70%	0.00%	5.61%	2.74%	NA
Tropical Japonica	504	99.00%	0.00%	0.99%	0.00%	NA
Japonica Intermediate	241	99.60%	0.00%	0.41%	0.00%	NA
VI/Aromatic	96	79.20%	0.00%	4.17%	16.67%	NA
Intermediate	90	82.20%	1.10%	4.44%	12.22%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0100239155	C -> A	LOC_Os01g01470.1	upstream_gene_variant ; 2486.0bp to feature; MODIFIER	silent_mutation	Average:36.056; most accessible tissue: Minghui63 panicle, score: 71.773	N	N	N	N
vg0100239155	C -> A	LOC_Os01g01460-LOC_Os01g01470	intergenic_region ; MODIFIER	silent_mutation	Average:36.056; most accessible tissue: Minghui63 panicle, score: 71.773	N	N	N	N
vg0100239155	C -> DEL	N	N	silent_mutation	Average:36.056; most accessible tissue: Minghui63 panicle, score: 71.773	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0100239155	7.41E-08	7.41E-08	mr1266	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