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Detailed information for vg0425095758:

Variant ID: vg0425095758 (JBrowse)	Variation Type: SNP
Chromosome: chr04	Position: 25095758
Reference Allele: T	Alternative Allele: C
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

GATAAAATTTTGTTAAATACTTCTCTTGTTTCTATAGTTCCTAGATTTTTCTGGGATTTATTTGAGCCAAGGAAGTATTTTTAATAAATGGAATTGCATT[T/C]
CATGAATAATTTAAAGGGAAAAAGGTTTTTAAAAGTCTTCTTTTGGCCCCAAAACCGCTCTCTCTCTCCCTCGGCCCAAGTCGGCCCAAGTCGAGCCGCC

Reverse complement sequence

GGCGGCTCGACTTGGGCCGACTTGGGCCGAGGGAGAGAGAGAGCGGTTTTGGGGCCAAAAGAAGACTTTTAAAAACCTTTTTCCCTTTAAATTATTCATG[A/G]
AATGCAATTCCATTTATTAAAAATACTTCCTTGGCTCAAATAAATCCCAGAAAAATCTAGGAACTATAGAAACAAGAGAAGTATTTAACAAAATTTTATC

Allele Frequencies:

Populations	Population Size	Frequency of T(primary allele)	Frequency of C(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	50.50%	1.70%	6.90%	40.90%	NA
All Indica	2759	25.80%	0.40%	8.34%	65.46%	NA
All Japonica	1512	91.30%	3.10%	4.43%	1.19%	NA
Aus	269	62.80%	0.00%	2.97%	34.20%	NA
Indica I	595	22.20%	0.00%	8.91%	68.91%	NA
Indica II	465	7.70%	0.40%	8.82%	83.01%	NA
Indica III	913	34.00%	0.80%	7.01%	58.27%	NA
Indica Intermediate	786	29.90%	0.10%	9.16%	60.81%	NA
Temperate Japonica	767	96.20%	0.50%	1.69%	1.56%	NA
Tropical Japonica	504	87.90%	6.30%	4.76%	0.99%	NA
Japonica Intermediate	241	82.60%	4.60%	12.45%	0.41%	NA
VI/Aromatic	96	74.00%	18.80%	7.29%	0.00%	NA
Intermediate	90	60.00%	5.60%	15.56%	18.89%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0425095758	T -> C	LOC_Os04g42399-LOC_Os04g42420	intergenic_region ; MODIFIER	silent_mutation	Average:12.377; most accessible tissue: Callus, score: 30.234	N	N	N	N
vg0425095758	T -> DEL	N	N	silent_mutation	Average:12.377; most accessible tissue: Callus, score: 30.234	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0425095758	2.29E-07	2.29E-07	mr1877_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