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Detailed information for vg0523543573:

Variant ID: vg0523543573 (JBrowse)	Variation Type: SNP
Chromosome: chr05	Position: 23543573
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: 126. )

Flanking Sequence (100 bp) in Reference Genome:

TAAAAACTATAAAATTAGAAATAGGAGGATGATAAGATTTGGTTTTTCAAAATCTTAAGACAACGAGATAACTATTTAATAAATTTGAAATAAAATCATA[T/C]
TAAAATATATATAATTTTATATTGGTGCTAGCAGTGCAATTGCGCGGGTCACCCAGCTAGTTATATTATTAAAACAGCTTTGAAAGGAGTCACCACGTTC

Reverse complement sequence

GAACGTGGTGACTCCTTTCAAAGCTGTTTTAATAATATAACTAGCTGGGTGACCCGCGCAATTGCACTGCTAGCACCAATATAAAATTATATATATTTTA[A/G]
TATGATTTTATTTCAAATTTATTAAATAGTTATCTCGTTGTCTTAAGATTTTGAAAAACCAAATCTTATCATCCTCCTATTTCTAATTTTATAGTTTTTA

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	87.10%	12.60%	0.30%	0.00%	NA
All Indica	2759	95.40%	4.50%	0.14%	0.00%	NA
All Japonica	1512	68.70%	30.80%	0.53%	0.00%	NA
Aus	269	99.60%	0.40%	0.00%	0.00%	NA
Indica I	595	100.00%	0.00%	0.00%	0.00%	NA
Indica II	465	95.30%	4.70%	0.00%	0.00%	NA
Indica III	913	90.80%	8.90%	0.33%	0.00%	NA
Indica Intermediate	786	97.30%	2.50%	0.13%	0.00%	NA
Temperate Japonica	767	94.90%	5.10%	0.00%	0.00%	NA
Tropical Japonica	504	31.70%	66.90%	1.39%	0.00%	NA
Japonica Intermediate	241	62.70%	36.90%	0.41%	0.00%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	90.00%	7.80%	2.22%	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
vg0523543573	T -> C	LOC_Os05g40070.1	upstream_gene_variant ; 4560.0bp to feature; MODIFIER	silent_mutation	Average:14.898; most accessible tissue: Minghui63 panicle, score: 20.733	N	N	N	N
vg0523543573	T -> C	LOC_Os05g40070-LOC_Os05g40080	intergenic_region ; MODIFIER	silent_mutation	Average:14.898; most accessible tissue: Minghui63 panicle, score: 20.733	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0523543573	NA	7.40E-07	mr1013	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
vg0523543573	NA	2.17E-06	mr1056	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
vg0523543573	2.14E-06	NA	mr1136	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
vg0523543573	1.31E-06	1.31E-06	mr1188	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
vg0523543573	NA	2.96E-11	mr1055_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
vg0523543573	NA	3.29E-13	mr1178_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
vg0523543573	NA	3.93E-06	mr1194_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
vg0523543573	NA	5.94E-08	mr1582_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
vg0523543573	NA	8.66E-07	mr1582_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
vg0523543573	NA	1.48E-07	mr1668_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