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Detailed information for vg0118504134:

Variant ID: vg0118504134 (JBrowse)	Variation Type: SNP
Chromosome: chr01	Position: 18504134
Reference Allele: C	Alternative Allele: T
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.91, C: 0.09, others allele: 0.00, population size: 96. )

Flanking Sequence (100 bp) in Reference Genome:

TCCGTAACCCCCCTCCCCTCATTATATTTTTGCTGGCGGTTTTTGCGTATGGCCGCCAGCAAAATTTATAGGGTAACGCCATGAAACATTACTTTTCTAG[C/T]
AGTGTATAAGACTTAGTATATGGTTAGTCCCGCCGAGCTTAATTAGTTGATTACTGTTGGGTATGGGTTATCCATAACCCTGACACATATTACCTTAAAA

Reverse complement sequence

TTTTAAGGTAATATGTGTCAGGGTTATGGATAACCCATACCCAACAGTAATCAACTAATTAAGCTCGGCGGGACTAACCATATACTAAGTCTTATACACT[G/A]
CTAGAAAAGTAATGTTTCATGGCGTTACCCTATAAATTTTGCTGGCGGCCATACGCAAAAACCGCCAGCAAAAATATAATGAGGGGAGGGGGGTTACGGA

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	59.50%	39.40%	0.53%	0.57%	NA
All Indica	2759	90.50%	8.10%	0.72%	0.72%	NA
All Japonica	1512	8.90%	91.10%	0.00%	0.07%	NA
Aus	269	53.90%	42.80%	1.12%	2.23%	NA
Indica I	595	95.30%	1.80%	2.52%	0.34%	NA
Indica II	465	82.60%	15.90%	0.22%	1.29%	NA
Indica III	913	91.50%	7.90%	0.00%	0.66%	NA
Indica Intermediate	786	90.30%	8.40%	0.51%	0.76%	NA
Temperate Japonica	767	1.30%	98.70%	0.00%	0.00%	NA
Tropical Japonica	504	14.70%	85.10%	0.00%	0.20%	NA
Japonica Intermediate	241	20.70%	79.30%	0.00%	0.00%	NA
VI/Aromatic	96	2.10%	97.90%	0.00%	0.00%	NA
Intermediate	90	41.10%	56.70%	2.22%	0.00%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0118504134	C -> T	LOC_Os01g33615.1	upstream_gene_variant ; 379.0bp to feature; MODIFIER	silent_mutation	Average:62.59; most accessible tissue: Minghui63 flag leaf, score: 77.828	N	N	N	N
vg0118504134	C -> T	LOC_Os01g33609.1	downstream_gene_variant ; 3719.0bp to feature; MODIFIER	silent_mutation	Average:62.59; most accessible tissue: Minghui63 flag leaf, score: 77.828	N	N	N	N
vg0118504134	C -> T	LOC_Os01g33630.1	downstream_gene_variant ; 2386.0bp to feature; MODIFIER	silent_mutation	Average:62.59; most accessible tissue: Minghui63 flag leaf, score: 77.828	N	N	N	N
vg0118504134	C -> T	LOC_Os01g33615-LOC_Os01g33630	intergenic_region ; MODIFIER	silent_mutation	Average:62.59; most accessible tissue: Minghui63 flag leaf, score: 77.828	N	N	N	N
vg0118504134	C -> DEL	N	N	silent_mutation	Average:62.59; most accessible tissue: Minghui63 flag leaf, score: 77.828	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0118504134	NA	2.84E-21	mr1698	All	Not	Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0118504134	4.93E-07	4.93E-07	mr1416_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
vg0118504134	NA	4.61E-46	mr1519_2	All	Not	Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0118504134	NA	6.66E-08	mr1645_2	All	Not	Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251