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Detailed information for vg0223926024:

Variant ID: vg0223926024 (JBrowse)	Variation Type: SNP
Chromosome: chr02	Position: 23926024
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

CCGAACAAGCAAACTACGGTTCTCATAAAATCAATAGGATGCAACCAAATGTAGATGTCTAGCCTGTAACCAAGATATTGTTTTTCGATAAATAGGGACA[C/T]
GAAACTCTTGAACTTAGTTCTAAGTCTACGATTAAAACGCCAGAGCACAGAAAAGCCGCAAGGTTTAAATGCATGCAAGTATTTCCTTTTCGAATCTGGG

Reverse complement sequence

CCCAGATTCGAAAAGGAAATACTTGCATGCATTTAAACCTTGCGGCTTTTCTGTGCTCTGGCGTTTTAATCGTAGACTTAGAACTAAGTTCAAGAGTTTC[G/A]
TGTCCCTATTTATCGAAAAACAATATCTTGGTTACAGGCTAGACATCTACATTTGGTTGCATCCTATTGATTTTATGAGAACCGTAGTTTGCTTGTTCGG

Allele Frequencies:

Populations	Population Size	Frequency of C(primary allele)	Frequency of T(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	79.10%	1.70%	3.41%	15.83%	NA
All Indica	2759	65.60%	2.40%	5.26%	26.68%	NA
All Japonica	1512	99.00%	0.30%	0.26%	0.40%	NA
Aus	269	97.40%	0.70%	1.86%	0.00%	NA
Indica I	595	35.10%	0.70%	6.05%	58.15%	NA
Indica II	465	70.80%	0.60%	2.37%	26.24%	NA
Indica III	913	76.30%	5.10%	6.57%	11.94%	NA
Indica Intermediate	786	73.30%	1.70%	4.83%	20.23%	NA
Temperate Japonica	767	99.70%	0.00%	0.00%	0.26%	NA
Tropical Japonica	504	97.80%	0.80%	0.60%	0.79%	NA
Japonica Intermediate	241	99.20%	0.40%	0.41%	0.00%	NA
VI/Aromatic	96	87.50%	7.30%	5.21%	0.00%	NA
Intermediate	90	91.10%	0.00%	2.22%	6.67%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0223926024	C -> T	LOC_Os02g39640-LOC_Os02g39650	intergenic_region ; MODIFIER	silent_mutation	Average:7.55; most accessible tissue: Callus, score: 26.784	N	N	N	N
vg0223926024	C -> DEL	N	N	silent_mutation	Average:7.55; most accessible tissue: Callus, score: 26.784	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0223926024	1.52E-06	NA	mr1124_2	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