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Detailed information for vg0123776584:

Variant ID: vg0123776584 (JBrowse)	Variation Type: SNP
Chromosome: chr01	Position: 23776584
Reference Allele: T	Alternative Allele: C
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 1.00, others allele: 0.00, population size: 103. )

Flanking Sequence (100 bp) in Reference Genome:

GACTATCACTAACACACAATGGCTAGAATGGCTAGAACTCCAGTTCATCCACGATCGTCCTCGATTGTAGCTGCATTCACTTACCTTTTGCTAGTCCTCT[T/C]
CCGAGACGCCATCACCACCGCAGCTGCATCTCCCAAAGCTCCGGCATCCACCAATGGCTGCATTGCAGCCGAGAGGGATGCCCTGCTCTCGTTCAAGGCT

Reverse complement sequence

AGCCTTGAACGAGAGCAGGGCATCCCTCTCGGCTGCAATGCAGCCATTGGTGGATGCCGGAGCTTTGGGAGATGCAGCTGCGGTGGTGATGGCGTCTCGG[A/G]
AGAGGACTAGCAAAAGGTAAGTGAATGCAGCTACAATCGAGGACGATCGTGGATGAACTGGAGTTCTAGCCATTCTAGCCATTGTGTGTTAGTGATAGTC

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	43.60%	0.10%	0.25%	56.12%	NA
All Indica	2759	9.90%	0.00%	0.29%	89.82%	NA
All Japonica	1512	92.10%	0.00%	0.00%	7.94%	NA
Aus	269	92.20%	0.00%	0.00%	7.81%	NA
Indica I	595	2.50%	0.00%	0.50%	96.97%	NA
Indica II	465	6.00%	0.00%	0.22%	93.76%	NA
Indica III	913	11.30%	0.00%	0.11%	88.61%	NA
Indica Intermediate	786	16.00%	0.10%	0.38%	83.46%	NA
Temperate Japonica	767	99.50%	0.00%	0.00%	0.52%	NA
Tropical Japonica	504	79.00%	0.00%	0.00%	21.03%	NA
Japonica Intermediate	241	95.90%	0.00%	0.00%	4.15%	NA
VI/Aromatic	96	99.00%	0.00%	0.00%	1.04%	NA
Intermediate	90	57.80%	2.20%	4.44%	35.56%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0123776584	T -> DEL	LOC_Os01g41930.1	N	frameshift_variant	Average:70.665; most accessible tissue: Minghui63 root, score: 86.528	N	N	N	N
vg0123776584	T -> C	LOC_Os01g41930.1	missense_variant ; p.Phe28Ser; MODERATE	nonsynonymous_codon ; F28S	Average:70.665; most accessible tissue: Minghui63 root, score: 86.528	unknown	unknown	TOLERATED	0.46

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0123776584	NA	1.05E-18	mr1422	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
vg0123776584	NA	2.92E-07	mr1850	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