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Detailed information for vg0431599339:

Variant ID: vg0431599339 (JBrowse)	Variation Type: SNP
Chromosome: chr04	Position: 31599339
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.95, T: 0.05, others allele: 0.00, population size: 74. )

Flanking Sequence (100 bp) in Reference Genome:

TACTGGCAAGTCGGAAAACAATCCTAGCATACTACATGTTGGCCATATTCAAAGATAAGCTGTGTATAGGTTAATTTGCATAAATGCCAATTTTAGTTCA[C/T]
AACATGTTTCGCAACGAAATTTTATAACGATAGTATAGAGTAAGTAAAACTTGTAATGTGAATGAATAAATAACACGCATCTACCCCTTAAGGTAGATCA

Reverse complement sequence

TGATCTACCTTAAGGGGTAGATGCGTGTTATTTATTCATTCACATTACAAGTTTTACTTACTCTATACTATCGTTATAAAATTTCGTTGCGAAACATGTT[G/A]
TGAACTAAAATTGGCATTTATGCAAATTAACCTATACACAGCTTATCTTTGAATATGGCCAACATGTAGTATGCTAGGATTGTTTTCCGACTTGCCAGTA

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	42.90%	13.30%	13.44%	30.32%	NA
All Indica	2759	27.10%	17.40%	16.13%	39.43%	NA
All Japonica	1512	71.80%	0.50%	8.47%	19.25%	NA
Aus	269	42.80%	33.50%	18.96%	4.83%	NA
Indica I	595	25.40%	43.00%	16.13%	15.46%	NA
Indica II	465	42.40%	4.10%	10.32%	43.23%	NA
Indica III	913	19.40%	8.10%	17.42%	55.09%	NA
Indica Intermediate	786	28.20%	16.50%	18.07%	37.15%	NA
Temperate Japonica	767	92.80%	0.10%	2.61%	4.43%	NA
Tropical Japonica	504	36.10%	0.20%	18.45%	45.24%	NA
Japonica Intermediate	241	79.30%	2.50%	6.22%	12.03%	NA
VI/Aromatic	96	36.50%	43.80%	2.08%	17.71%	NA
Intermediate	90	52.20%	11.10%	10.00%	26.67%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0431599339	C -> DEL	N	N	silent_mutation	Average:23.483; most accessible tissue: Zhenshan97 root, score: 47.644	N	N	N	N
vg0431599339	C -> T	LOC_Os04g53050.1	upstream_gene_variant ; 782.0bp to feature; MODIFIER	silent_mutation	Average:23.483; most accessible tissue: Zhenshan97 root, score: 47.644	N	N	N	N
vg0431599339	C -> T	LOC_Os04g53040.1	downstream_gene_variant ; 1555.0bp to feature; MODIFIER	silent_mutation	Average:23.483; most accessible tissue: Zhenshan97 root, score: 47.644	N	N	N	N
vg0431599339	C -> T	LOC_Os04g53040-LOC_Os04g53050	intergenic_region ; MODIFIER	silent_mutation	Average:23.483; most accessible tissue: Zhenshan97 root, score: 47.644	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0431599339	1.42E-06	NA	mr1800_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