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Detailed information for vg0502284343:

Variant ID: vg0502284343 (JBrowse)	Variation Type: SNP
Chromosome: chr05	Position: 2284343
Reference Allele: C	Alternative Allele: T
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.77, T: 0.23, others allele: 0.00, population size: 96. )

Flanking Sequence (100 bp) in Reference Genome:

CCGCACGCATCCAAGGGTATGCGAAAATCATGATTTTTGCGTGCGGGTGCTTACCTGCAAGGGAAAATAAAAATCCGAAAAAAAATAAAATTTCAAAAAA[C/T]
GAATCCGGCGTCCCGGCCGCCGCCGCTCCCGGCCGCCGCCGCCTCCTCCTCCTCCTCCTCCTCCTCCTCGTCGTCCTCATCATCGTCGTCGTCAGCCAAC

Reverse complement sequence

GTTGGCTGACGACGACGATGATGAGGACGACGAGGAGGAGGAGGAGGAGGAGGAGGAGGCGGCGGCGGCCGGGAGCGGCGGCGGCCGGGACGCCGGATTC[G/A]
TTTTTTGAAATTTTATTTTTTTTCGGATTTTTATTTTCCCTTGCAGGTAAGCACCCGCACGCAAAAATCATGATTTTCGCATACCCTTGGATGCGTGCGG

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	54.20%	45.30%	0.51%	0.00%	NA
All Indica	2759	69.20%	30.40%	0.43%	0.00%	NA
All Japonica	1512	28.20%	71.80%	0.00%	0.00%	NA
Aus	269	61.70%	36.40%	1.86%	0.00%	NA
Indica I	595	99.70%	0.30%	0.00%	0.00%	NA
Indica II	465	79.10%	20.60%	0.22%	0.00%	NA
Indica III	913	44.40%	55.00%	0.66%	0.00%	NA
Indica Intermediate	786	69.00%	30.40%	0.64%	0.00%	NA
Temperate Japonica	767	6.60%	93.40%	0.00%	0.00%	NA
Tropical Japonica	504	61.10%	38.90%	0.00%	0.00%	NA
Japonica Intermediate	241	28.20%	71.80%	0.00%	0.00%	NA
VI/Aromatic	96	13.50%	82.30%	4.17%	0.00%	NA
Intermediate	90	52.20%	44.40%	3.33%	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
vg0502284343	C -> T	LOC_Os05g04790.1	downstream_gene_variant ; 4295.0bp to feature; MODIFIER	silent_mutation	Average:73.535; most accessible tissue: Zhenshan97 flag leaf, score: 82.703	N	N	N	N
vg0502284343	C -> T	LOC_Os05g04790-LOC_Os05g04810	intergenic_region ; MODIFIER	silent_mutation	Average:73.535; most accessible tissue: Zhenshan97 flag leaf, score: 82.703	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0502284343	NA	6.11E-06	mr1120	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
vg0502284343	6.78E-06	NA	mr1301	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
vg0502284343	NA	4.57E-07	mr1045_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
vg0502284343	NA	5.63E-06	mr1109_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
vg0502284343	9.60E-06	NA	mr1301_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
vg0502284343	NA	7.49E-08	mr1423_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
vg0502284343	NA	9.92E-07	mr1570_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
vg0502284343	NA	2.54E-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
vg0502284343	NA	1.38E-06	mr1785_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
vg0502284343	NA	6.91E-12	mr1789_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
vg0502284343	NA	1.44E-08	mr1837_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
vg0502284343	NA	6.45E-12	mr1844_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
vg0502284343	NA	8.35E-06	mr1844_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
vg0502284343	NA	4.19E-06	mr1957_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