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Detailed information for vg0101794928:

Variant ID: vg0101794928 (JBrowse)	Variation Type: SNP
Chromosome: chr01	Position: 1794928
Reference Allele: T	Alternative Allele: C
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

AGTCATATGGATGAGTTTTATAGAAGTTTTCAGTTCTTGCTAGTCTGATGAATGCCGGTAGGTTGTTGTTGTGTGTGAATTGTGTTGGTTTTCATCCATC[T/C]
ATCTATCTATCTATCTATCTATCTATCTATCTATCTATTATCTATCTATTATATACTAAAAGTCCATTAAACTTCCTTAAAACGCTCTCAAGCTGCCATG

Reverse complement sequence

CATGGCAGCTTGAGAGCGTTTTAAGGAAGTTTAATGGACTTTTAGTATATAATAGATAGATAATAGATAGATAGATAGATAGATAGATAGATAGATAGAT[A/G]
GATGGATGAAAACCAACACAATTCACACACAACAACAACCTACCGGCATTCATCAGACTAGCAAGAACTGAAAACTTCTATAAAACTCATCCATATGACT

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	34.90%	2.60%	4.51%	58.00%	NA
All Indica	2759	12.10%	0.10%	3.88%	83.91%	NA
All Japonica	1512	65.80%	7.70%	3.44%	23.08%	NA
Aus	269	74.00%	0.00%	11.90%	14.13%	NA
Indica I	595	4.40%	0.00%	3.36%	92.27%	NA
Indica II	465	18.50%	0.40%	1.08%	80.00%	NA
Indica III	913	13.60%	0.00%	4.82%	81.60%	NA
Indica Intermediate	786	12.50%	0.10%	4.83%	82.57%	NA
Temperate Japonica	767	80.80%	0.10%	1.04%	17.99%	NA
Tropical Japonica	504	53.00%	20.60%	6.75%	19.64%	NA
Japonica Intermediate	241	44.80%	4.60%	4.15%	46.47%	NA
VI/Aromatic	96	81.20%	0.00%	14.58%	4.17%	NA
Intermediate	90	48.90%	3.30%	8.89%	38.89%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0101794928	T -> DEL	N	N	silent_mutation	Average:48.41; most accessible tissue: Minghui63 root, score: 86.159	N	N	N	N
vg0101794928	T -> C	LOC_Os01g04110.1	upstream_gene_variant ; 3430.0bp to feature; MODIFIER	silent_mutation	Average:48.41; most accessible tissue: Minghui63 root, score: 86.159	N	N	N	N
vg0101794928	T -> C	LOC_Os01g04110-LOC_Os01g04120	intergenic_region ; MODIFIER	silent_mutation	Average:48.41; most accessible tissue: Minghui63 root, score: 86.159	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0101794928	3.79E-06	2.31E-06	mr1595_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