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Detailed information for vg0128529665:

Variant ID: vg0128529665 (JBrowse)	Variation Type: SNP
Chromosome: chr01	Position: 28529665
Reference Allele: T	Alternative Allele: C
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 1.00, others allele: 0.00, population size: 49. )

Flanking Sequence (100 bp) in Reference Genome:

TGCTGCCGCTCCTCCTTGTCTTGGTTGCCGCTTCCCATGGCGCTTCCAATGACACCTACGACACCTCCATGTGCCTGCAGGAAACAACCACCTGCGGGGA[T/C]
GTCAGTATCAGATACCCGTTCTACTTTTCTGATAAGACGGGATATATCAACGGGTCCAGCAACTCATACTGCGGATACCCCGGCCTGGCGATCGATTGTG

Reverse complement sequence

CACAATCGATCGCCAGGCCGGGGTATCCGCAGTATGAGTTGCTGGACCCGTTGATATATCCCGTCTTATCAGAAAAGTAGAACGGGTATCTGATACTGAC[A/G]
TCCCCGCAGGTGGTTGTTTCCTGCAGGCACATGGAGGTGTCGTAGGTGTCATTGGAAGCGCCATGGGAAGCGGCAACCAAGACAAGGAGGAGCGGCAGCA

Allele Frequencies:

Populations	Population Size	Frequency of C(primary allele)	Frequency of T(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	74.10%	24.00%	0.59%	1.25%	NA
All Indica	2759	97.50%	1.00%	0.07%	1.38%	NA
All Japonica	1512	26.50%	70.50%	1.72%	1.32%	NA
Aus	269	99.60%	0.40%	0.00%	0.00%	NA
Indica I	595	98.50%	1.20%	0.00%	0.34%	NA
Indica II	465	97.80%	1.70%	0.43%	0.00%	NA
Indica III	913	95.90%	0.20%	0.00%	3.83%	NA
Indica Intermediate	786	98.50%	1.40%	0.00%	0.13%	NA
Temperate Japonica	767	7.20%	89.60%	0.91%	2.35%	NA
Tropical Japonica	504	63.10%	33.10%	3.77%	0.00%	NA
Japonica Intermediate	241	11.20%	88.00%	0.00%	0.83%	NA
VI/Aromatic	96	86.50%	13.50%	0.00%	0.00%	NA
Intermediate	90	68.90%	30.00%	0.00%	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
vg0128529665	T -> DEL	N	N	silent_mutation	Average:14.211; most accessible tissue: Callus, score: 32.289	N	N	N	N
vg0128529665	T -> C	LOC_Os01g49614.2	downstream_gene_variant ; 2181.0bp to feature; MODIFIER	silent_mutation	Average:14.211; most accessible tissue: Callus, score: 32.289	N	N	N	N
vg0128529665	T -> C	LOC_Os01g49614.1	intron_variant ; MODIFIER	silent_mutation	Average:14.211; most accessible tissue: Callus, score: 32.289	N	N	N	N
vg0128529665	T -> C	LOC_Os01g49614.3	intron_variant ; MODIFIER	silent_mutation	Average:14.211; most accessible tissue: Callus, score: 32.289	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0128529665	NA	1.64E-07	mr1156	Jap_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
vg0128529665	NA	1.56E-07	mr1596	Jap_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
vg0128529665	NA	5.89E-06	mr1060_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
vg0128529665	NA	1.64E-06	mr1115_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
vg0128529665	NA	2.61E-06	mr1204_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
vg0128529665	NA	4.56E-08	mr1296_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
vg0128529665	NA	1.28E-06	mr1358_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
vg0128529665	NA	3.26E-09	mr1378_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
vg0128529665	NA	7.09E-07	mr1528_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
vg0128529665	NA	3.17E-08	mr1555_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
vg0128529665	NA	5.48E-07	mr1571_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
vg0128529665	3.13E-06	3.13E-06	mr1574_2	Jap_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
vg0128529665	NA	2.34E-06	mr1661_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
vg0128529665	NA	6.30E-10	mr1743_2	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
vg0128529665	NA	1.31E-07	mr1743_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
vg0128529665	NA	3.47E-08	mr1748_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
vg0128529665	NA	4.58E-06	mr1756_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
vg0128529665	NA	6.37E-06	mr1763_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
vg0128529665	NA	3.67E-07	mr1880_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