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Detailed information for vg0135985571:

Variant ID: vg0135985571 (JBrowse)	Variation Type: SNP
Chromosome: chr01	Position: 35985571
Reference Allele: C	Alternative Allele: T
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.93, T: 0.06, others allele: 0.00, population size: 241. )

Flanking Sequence (100 bp) in Reference Genome:

TCGCAGTGGCGTTAGTCGAGCATATCATAAATTATTTGGCAGGGAACTTGAAAGCATAAAAGGGAAAATTCAGATATATTGAAATTCAAAGAATTCGATT[C/T]
GTTCTCCTCATATTGAAATTAGAAGGGCAGAGGAAGAAACGGGGTAAACCTTATGATAGCAAATTTAACAGAAGAGATTCAAATCTAATAGAACATGGTC

Reverse complement sequence

GACCATGTTCTATTAGATTTGAATCTCTTCTGTTAAATTTGCTATCATAAGGTTTACCCCGTTTCTTCCTCTGCCCTTCTAATTTCAATATGAGGAGAAC[G/A]
AATCGAATTCTTTGAATTTCAATATATCTGAATTTTCCCTTTTATGCTTTCAAGTTCCCTGCCAAATAATTTATGATATGCTCGACTAACGCCACTGCGA

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	61.70%	38.20%	0.17%	0.00%	NA
All Indica	2759	94.50%	5.30%	0.25%	0.00%	NA
All Japonica	1512	2.10%	97.90%	0.00%	0.00%	NA
Aus	269	58.70%	41.30%	0.00%	0.00%	NA
Indica I	595	90.60%	9.10%	0.34%	0.00%	NA
Indica II	465	99.40%	0.40%	0.22%	0.00%	NA
Indica III	913	97.40%	2.60%	0.00%	0.00%	NA
Indica Intermediate	786	91.10%	8.40%	0.51%	0.00%	NA
Temperate Japonica	767	1.30%	98.70%	0.00%	0.00%	NA
Tropical Japonica	504	2.80%	97.20%	0.00%	0.00%	NA
Japonica Intermediate	241	3.30%	96.70%	0.00%	0.00%	NA
VI/Aromatic	96	83.30%	16.70%	0.00%	0.00%	NA
Intermediate	90	43.30%	55.60%	1.11%	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
vg0135985571	C -> T	LOC_Os01g62160.1	intron_variant ; MODIFIER	silent_mutation	Average:38.163; most accessible tissue: Callus, score: 65.033	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0135985571	NA	4.06E-08	mr1260	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
vg0135985571	NA	3.66E-10	mr1714	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
vg0135985571	NA	4.89E-06	mr1746_2	Ind_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