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Detailed information for vg0810040454:

Variant ID: vg0810040454 (JBrowse)	Variation Type: SNP
Chromosome: chr08	Position: 10040454
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.96, T: 0.03, others allele: 0.00, population size: 103. )

Flanking Sequence (100 bp) in Reference Genome:

GGCTTTACTTAGGGCCCGATTGAGATAGATTCATCCGTGACGGCTGTTTGCCCGATTGAGATAACTCTTCACATCAGTGACTTCTAGCCTGTGACGGATG[C/T]
TGTGCCTGATTGAGATGAGGGTATCCGTTATAGTGTATACTACATATATGGTTAAAATTGCTTTATAACTGAAATAGTAAGGAGGATATATATGCGTGAA

Reverse complement sequence

TTCACGCATATATATCCTCCTTACTATTTCAGTTATAAAGCAATTTTAACCATATATGTAGTATACACTATAACGGATACCCTCATCTCAATCAGGCACA[G/A]
CATCCGTCACAGGCTAGAAGTCACTGATGTGAAGAGTTATCTCAATCGGGCAAACAGCCGTCACGGATGAATCTATCTCAATCGGGCCCTAAGTAAAGCC

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	45.60%	28.40%	0.38%	25.62%	NA
All Indica	2759	34.70%	46.40%	0.51%	18.38%	NA
All Japonica	1512	58.20%	2.10%	0.20%	39.55%	NA
Aus	269	97.00%	1.10%	0.37%	1.49%	NA
Indica I	595	49.20%	46.60%	0.17%	4.03%	NA
Indica II	465	39.60%	40.20%	0.43%	19.78%	NA
Indica III	913	25.50%	45.80%	0.33%	28.37%	NA
Indica Intermediate	786	31.60%	50.60%	1.02%	16.79%	NA
Temperate Japonica	767	89.20%	1.80%	0.00%	9.00%	NA
Tropical Japonica	504	18.30%	2.20%	0.60%	78.97%	NA
Japonica Intermediate	241	43.20%	2.50%	0.00%	54.36%	NA
VI/Aromatic	96	10.40%	7.30%	0.00%	82.29%	NA
Intermediate	90	52.20%	22.20%	0.00%	25.56%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0810040454	C -> T	LOC_Os08g16410.1	upstream_gene_variant ; 4031.0bp to feature; MODIFIER	silent_mutation	Average:63.666; most accessible tissue: Minghui63 root, score: 76.119	N	N	N	N
vg0810040454	C -> T	LOC_Os08g16420.1	downstream_gene_variant ; 547.0bp to feature; MODIFIER	silent_mutation	Average:63.666; most accessible tissue: Minghui63 root, score: 76.119	N	N	N	N
vg0810040454	C -> T	LOC_Os08g16420-LOC_Os08g16430	intergenic_region ; MODIFIER	silent_mutation	Average:63.666; most accessible tissue: Minghui63 root, score: 76.119	N	N	N	N
vg0810040454	C -> DEL	N	N	silent_mutation	Average:63.666; most accessible tissue: Minghui63 root, score: 76.119	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0810040454	6.82E-07	1.73E-07	mr1134	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
vg0810040454	NA	1.99E-06	mr1135	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
vg0810040454	2.35E-06	3.91E-07	mr1504	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