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Detailed information for vg0102504990:

Variant ID: vg0102504990 (JBrowse)	Variation Type: SNP
Chromosome: chr01	Position: 2504990
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

GTCGACGGGTACGTCGTCTACCACTGAAAGAATAATTAGCCGTAAATGCGAGCACCCGTGTCAAATCTAGGATTTGAACCCAGGTGGGCTGGTTCCACCA[C/T]
AAGGAACCTAACCAGTTGAGCTATACTCACTTCGCATGATACAAATGATTTCATCTGAGCACGTAAGGTTGCTTCTACATAAGGTTTTGTGTTACCATCA

Reverse complement sequence

TGATGGTAACACAAAACCTTATGTAGAAGCAACCTTACGTGCTCAGATGAAATCATTTGTATCATGCGAAGTGAGTATAGCTCAACTGGTTAGGTTCCTT[G/A]
TGGTGGAACCAGCCCACCTGGGTTCAAATCCTAGATTTGACACGGGTGCTCGCATTTACGGCTAATTATTCTTTCAGTGGTAGACGACGTACCCGTCGAC

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	44.90%	3.40%	1.40%	50.34%	NA
All Indica	2759	26.90%	4.40%	1.34%	67.38%	NA
All Japonica	1512	77.00%	2.40%	0.26%	20.30%	NA
Aus	269	29.40%	0.00%	8.18%	62.45%	NA
Indica I	595	9.70%	0.80%	0.67%	88.74%	NA
Indica II	465	33.50%	0.20%	2.37%	63.87%	NA
Indica III	913	33.60%	8.50%	0.88%	56.96%	NA
Indica Intermediate	786	28.10%	4.70%	1.78%	65.39%	NA
Temperate Japonica	767	82.40%	0.00%	0.13%	17.47%	NA
Tropical Japonica	504	70.40%	6.70%	0.60%	22.22%	NA
Japonica Intermediate	241	73.40%	1.20%	0.00%	25.31%	NA
VI/Aromatic	96	80.20%	0.00%	1.04%	18.75%	NA
Intermediate	90	65.60%	2.20%	2.22%	30.00%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0102504990	C -> T	LOC_Os01g05310.1	downstream_gene_variant ; 3741.0bp to feature; MODIFIER	silent_mutation	Average:17.483; most accessible tissue: Callus, score: 57.418	N	N	N	N
vg0102504990	C -> T	LOC_Os01g05320.1	intron_variant ; MODIFIER	silent_mutation	Average:17.483; most accessible tissue: Callus, score: 57.418	N	N	N	N
vg0102504990	C -> DEL	N	N	silent_mutation	Average:17.483; most accessible tissue: Callus, score: 57.418	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0102504990	4.64E-06	2.15E-06	mr1693	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