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Detailed information for vg0805485086:

Variant ID: vg0805485086 (JBrowse)	Variation Type: SNP
Chromosome: chr08	Position: 5485086
Reference Allele: C	Alternative Allele: T
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

ATAAAAGTTTCTTTGGTTTTTCTATACTTAATTCCTACAAACCGAATGACCCTTAGGAATACAAATAATTTATTTTCCCTCCAAACCGAACAAGCCATAA[C/T]
AAGAACAAATTAACAAATTAAATCGATCACAGAACACAATGCTGCACAAAAACAGCCTAACCTGGTATGTAAGGGTATTTTCAAGAGGATGAAATAATAA

Reverse complement sequence

TTATTATTTCATCCTCTTGAAAATACCCTTACATACCAGGTTAGGCTGTTTTTGTGCAGCATTGTGTTCTGTGATCGATTTAATTTGTTAATTTGTTCTT[G/A]
TTATGGCTTGTTCGGTTTGGAGGGAAAATAAATTATTTGTATTCCTAAGGGTCATTCGGTTTGTAGGAATTAAGTATAGAAAAACCAAAGAAACTTTTAT

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	47.20%	28.10%	0.55%	24.14%	NA
All Indica	2759	67.40%	0.80%	0.80%	30.95%	NA
All Japonica	1512	2.00%	84.60%	0.13%	13.29%	NA
Aus	269	98.90%	0.00%	0.00%	1.12%	NA
Indica I	595	57.30%	0.30%	0.34%	42.02%	NA
Indica II	465	52.70%	2.60%	0.65%	44.09%	NA
Indica III	913	84.40%	0.20%	1.42%	13.91%	NA
Indica Intermediate	786	64.00%	0.90%	0.51%	34.61%	NA
Temperate Japonica	767	0.40%	96.00%	0.13%	3.52%	NA
Tropical Japonica	504	4.00%	71.00%	0.20%	24.80%	NA
Japonica Intermediate	241	2.90%	76.80%	0.00%	20.33%	NA
VI/Aromatic	96	38.50%	0.00%	0.00%	61.46%	NA
Intermediate	90	42.20%	28.90%	2.22%	26.67%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0805485086	C -> T	LOC_Os08g09460.1	upstream_gene_variant ; 3199.0bp to feature; MODIFIER	silent_mutation	Average:31.604; most accessible tissue: Minghui63 panicle, score: 46.754	N	N	N	N
vg0805485086	C -> T	LOC_Os08g09470.1	downstream_gene_variant ; 376.0bp to feature; MODIFIER	silent_mutation	Average:31.604; most accessible tissue: Minghui63 panicle, score: 46.754	N	N	N	N
vg0805485086	C -> T	LOC_Os08g09460-LOC_Os08g09470	intergenic_region ; MODIFIER	silent_mutation	Average:31.604; most accessible tissue: Minghui63 panicle, score: 46.754	N	N	N	N
vg0805485086	C -> DEL	N	N	silent_mutation	Average:31.604; most accessible tissue: Minghui63 panicle, score: 46.754	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0805485086	NA	8.75E-06	mr1268	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
vg0805485086	NA	2.05E-07	mr1414	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
vg0805485086	NA	7.40E-18	mr1529	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
vg0805485086	NA	4.89E-15	mr1162_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
vg0805485086	NA	8.79E-24	mr1350_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
vg0805485086	7.22E-06	NA	mr1368_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
vg0805485086	NA	9.87E-16	mr1529_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
vg0805485086	NA	8.38E-06	mr1567_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
vg0805485086	NA	7.55E-14	mr1575_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
vg0805485086	8.49E-06	NA	mr1584_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
vg0805485086	NA	3.56E-11	mr1722_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
vg0805485086	NA	4.82E-08	mr1806_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
vg0805485086	8.23E-06	8.23E-06	mr1846_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
vg0805485086	NA	8.55E-13	mr1853_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
vg0805485086	NA	5.80E-07	mr1853_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
vg0805485086	5.02E-07	5.02E-07	mr1954_2	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