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Detailed information for vg0600619985:

Variant ID: vg0600619985 (JBrowse)	Variation Type: SNP
Chromosome: chr06	Position: 619985
Reference Allele: A	Alternative Allele: C
Primary Allele: A	Secondary Allele: C

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.98, C: 0.01, others allele: 0.00, population size: 254. )

Flanking Sequence (100 bp) in Reference Genome:

GATTCCTGCTATATTCGGTTAAGGAAATCAATCTACTAAAGGAAGTTTATCCATAAGCAACCGAGTTCAAAGAGGATGCGGCATGGCAGTTTATCTATTA[A/C]
TTAGGAATAGTTTGTTAGTTTCCTTTTATCTTTAGGAAAGTGTGTTTAGTGTCCGATAAGGACTTTATGTTTTCCTTTTATCTTTAGTTTCTTTCTTGTC

Reverse complement sequence

GACAAGAAAGAAACTAAAGATAAAAGGAAAACATAAAGTCCTTATCGGACACTAAACACACTTTCCTAAAGATAAAAGGAAACTAACAAACTATTCCTAA[T/G]
TAATAGATAAACTGCCATGCCGCATCCTCTTTGAACTCGGTTGCTTATGGATAAACTTCCTTTAGTAGATTGATTTCCTTAACCGAATATAGCAGGAATC

Allele Frequencies:

Populations	Population Size	Frequency of A(primary allele)	Frequency of C(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	82.10%	12.10%	1.25%	4.57%	NA
All Indica	2759	72.70%	18.10%	1.45%	7.72%	NA
All Japonica	1512	97.00%	2.20%	0.73%	0.07%	NA
Aus	269	84.80%	12.30%	2.60%	0.37%	NA
Indica I	595	92.60%	6.20%	0.67%	0.50%	NA
Indica II	465	94.00%	4.30%	0.43%	1.29%	NA
Indica III	913	45.30%	33.80%	1.97%	18.84%	NA
Indica Intermediate	786	76.80%	17.00%	2.04%	4.07%	NA
Temperate Japonica	767	100.00%	0.00%	0.00%	0.00%	NA
Tropical Japonica	504	91.90%	5.80%	2.18%	0.20%	NA
Japonica Intermediate	241	98.30%	1.70%	0.00%	0.00%	NA
VI/Aromatic	96	97.90%	2.10%	0.00%	0.00%	NA
Intermediate	90	92.20%	5.60%	1.11%	1.11%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0600619985	A -> C	LOC_Os06g02090.1	downstream_gene_variant ; 1121.0bp to feature; MODIFIER	silent_mutation	Average:34.754; most accessible tissue: Minghui63 panicle, score: 50.413	N	N	N	N
vg0600619985	A -> C	LOC_Os06g02100.1	downstream_gene_variant ; 3477.0bp to feature; MODIFIER	silent_mutation	Average:34.754; most accessible tissue: Minghui63 panicle, score: 50.413	N	N	N	N
vg0600619985	A -> C	LOC_Os06g02090-LOC_Os06g02100	intergenic_region ; MODIFIER	silent_mutation	Average:34.754; most accessible tissue: Minghui63 panicle, score: 50.413	N	N	N	N
vg0600619985	A -> DEL	N	N	silent_mutation	Average:34.754; most accessible tissue: Minghui63 panicle, score: 50.413	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0600619985	NA	1.50E-06	mr1260_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