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Detailed information for vg0113601714:

Variant ID: vg0113601714 (JBrowse)	Variation Type: SNP
Chromosome: chr01	Position: 13601714
Reference Allele: T	Alternative Allele: C
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.62, C: 0.38, others allele: 0.00, population size: 34. )

Flanking Sequence (100 bp) in Reference Genome:

AGTTCATTCTTGTTGTCGTAGAAGAGACCTCTTGCGTTGCAGACATCACGACGGAGGAATCGGCAGAGGTCAGCGCCCACGTTCCAGGTAGTACCGTTGT[T/C]
GATTTGTTGTGCAATATATGGGATTTCGGGGATCTGCGCACAGAAAGGAAAATAGAATGGTACTCAGTGAGAAGCGTGTGCTAGATGGGTTTCTTTGTAG

Reverse complement sequence

CTACAAAGAAACCCATCTAGCACACGCTTCTCACTGAGTACCATTCTATTTTCCTTTCTGTGCGCAGATCCCCGAAATCCCATATATTGCACAACAAATC[A/G]
ACAACGGTACTACCTGGAACGTGGGCGCTGACCTCTGCCGATTCCTCCGTCGTGATGTCTGCAACGCAAGAGGTCTCTTCTACGACAACAAGAATGAACT

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	41.20%	24.10%	9.44%	25.33%	NA
All Indica	2759	17.50%	38.10%	11.34%	33.06%	NA
All Japonica	1512	86.70%	0.90%	1.79%	10.58%	NA
Aus	269	29.00%	17.50%	33.09%	20.45%	NA
Indica I	595	27.90%	37.60%	9.92%	24.54%	NA
Indica II	465	13.30%	45.60%	10.32%	30.75%	NA
Indica III	913	11.10%	33.80%	13.47%	41.62%	NA
Indica Intermediate	786	19.60%	38.90%	10.56%	30.92%	NA
Temperate Japonica	767	98.70%	0.10%	0.00%	1.17%	NA
Tropical Japonica	504	65.30%	2.00%	4.96%	27.78%	NA
Japonica Intermediate	241	93.40%	1.20%	0.83%	4.56%	NA
VI/Aromatic	96	30.20%	9.40%	5.21%	55.21%	NA
Intermediate	90	48.90%	18.90%	13.33%	18.89%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0113601714	T -> DEL	LOC_Os01g24130.1	N	frameshift_variant	Average:36.429; most accessible tissue: Callus, score: 50.838	N	N	N	N
vg0113601714	T -> C	LOC_Os01g24130.1	missense_variant ; p.Asn407Asp; MODERATE	nonsynonymous_codon	Average:36.429; most accessible tissue: Callus, score: 50.838	unknown	unknown	TOLERATED	0.76

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0113601714	NA	7.49E-06	mr1786_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