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Detailed information for vg0226725058:

Variant ID: vg0226725058 (JBrowse)	Variation Type: SNP
Chromosome: chr02	Position: 26725058
Reference Allele: C	Alternative Allele: A
Primary Allele: C	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

TACTCACCCTTGCAATATACAAACTTAATCAGAGGTCGGAGATGAAGCTTCGGAGGATCCCTATGCCTATTACTAGGAGGGTGATGAAGACGATGGCGCT[C/A]
AGTAGGTCTTAGTTACGGTCATTGCCTGTGGCAATGGCGTGCCGCTGCCTTAACTCCGCTGCCTTATCTACTTCTGTTTTTGGGATGTATTCTGGACCGC

Reverse complement sequence

GCGGTCCAGAATACATCCCAAAAACAGAAGTAGATAAGGCAGCGGAGTTAAGGCAGCGGCACGCCATTGCCACAGGCAATGACCGTAACTAAGACCTACT[G/T]
AGCGCCATCGTCTTCATCACCCTCCTAGTAATAGGCATAGGGATCCTCCGAAGCTTCATCTCCGACCTCTGATTAAGTTTGTATATTGCAAGGGTGAGTA

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	40.00%	1.30%	7.64%	51.06%	NA
All Indica	2759	10.30%	0.00%	8.99%	80.65%	NA
All Japonica	1512	95.20%	3.80%	0.46%	0.46%	NA
Aus	269	7.10%	0.00%	37.55%	55.39%	NA
Indica I	595	5.40%	0.00%	9.41%	85.21%	NA
Indica II	465	5.20%	0.00%	14.19%	80.65%	NA
Indica III	913	17.30%	0.10%	6.57%	76.01%	NA
Indica Intermediate	786	9.00%	0.00%	8.40%	82.57%	NA
Temperate Japonica	767	99.60%	0.00%	0.26%	0.13%	NA
Tropical Japonica	504	87.50%	11.10%	0.20%	1.19%	NA
Japonica Intermediate	241	97.50%	0.80%	1.66%	0.00%	NA
VI/Aromatic	96	95.80%	0.00%	0.00%	4.17%	NA
Intermediate	90	62.20%	1.10%	5.56%	31.11%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0226725058	C -> A	LOC_Os02g44140.1	upstream_gene_variant ; 2786.0bp to feature; MODIFIER	silent_mutation	Average:16.433; most accessible tissue: Zhenshan97 panicle, score: 28.447	N	N	N	N
vg0226725058	C -> A	LOC_Os02g44155.1	upstream_gene_variant ; 1542.0bp to feature; MODIFIER	silent_mutation	Average:16.433; most accessible tissue: Zhenshan97 panicle, score: 28.447	N	N	N	N
vg0226725058	C -> A	LOC_Os02g44150.1	downstream_gene_variant ; 255.0bp to feature; MODIFIER	silent_mutation	Average:16.433; most accessible tissue: Zhenshan97 panicle, score: 28.447	N	N	N	N
vg0226725058	C -> A	LOC_Os02g44140-LOC_Os02g44150	intergenic_region ; MODIFIER	silent_mutation	Average:16.433; most accessible tissue: Zhenshan97 panicle, score: 28.447	N	N	N	N
vg0226725058	C -> DEL	N	N	silent_mutation	Average:16.433; 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
vg0226725058	NA	8.35E-06	mr1553_2	Jap_All	Not	Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0226725058	4.56E-06	4.56E-06	mr1574_2	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