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Detailed information for vg0620312022:

Variant ID: vg0620312022 (JBrowse)	Variation Type: SNP
Chromosome: chr06	Position: 20312022
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.01, others allele: 0.00, population size: 209. )

Flanking Sequence (100 bp) in Reference Genome:

AAATGTGGTTGTACGGTGTCGTTTCATGCTTAACTTCATGGCTTGGTCTTTAATTGACCAGGGACGGTACTAGCCTTTCCCGGATACCACCCAAATCCAC[C/T]
GTCCGCCCCGGTCTAAAACAAAGGTTTTTAATTCCTTTCATGTCATCATTATCATGGCAATGTGGTGCTCATATCTCCACATGCCGCATCTTAATTACCT

Reverse complement sequence

AGGTAATTAAGATGCGGCATGTGGAGATATGAGCACCACATTGCCATGATAATGATGACATGAAAGGAATTAAAAACCTTTGTTTTAGACCGGGGCGGAC[G/A]
GTGGATTTGGGTGGTATCCGGGAAAGGCTAGTACCGTCCCTGGTCAATTAAAGACCAAGCCATGAAGTTAAGCATGAAACGACACCGTACAACCACATTT

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	56.20%	3.00%	16.65%	24.08%	NA
All Indica	2759	33.40%	5.10%	23.70%	37.77%	NA
All Japonica	1512	97.40%	0.00%	1.72%	0.86%	NA
Aus	269	55.40%	0.40%	26.02%	18.22%	NA
Indica I	595	26.10%	0.80%	32.44%	40.67%	NA
Indica II	465	31.40%	1.90%	22.80%	43.87%	NA
Indica III	913	37.50%	10.60%	19.50%	32.42%	NA
Indica Intermediate	786	35.40%	3.90%	22.52%	38.17%	NA
Temperate Japonica	767	96.70%	0.00%	1.96%	1.30%	NA
Tropical Japonica	504	99.00%	0.00%	0.60%	0.40%	NA
Japonica Intermediate	241	96.30%	0.00%	3.32%	0.41%	NA
VI/Aromatic	96	56.20%	0.00%	27.08%	16.67%	NA
Intermediate	90	67.80%	0.00%	12.22%	20.00%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0620312022	C -> T	LOC_Os06g34920.1	upstream_gene_variant ; 328.0bp to feature; MODIFIER	silent_mutation	Average:6.719; most accessible tissue: Callus, score: 17.666	N	N	N	N
vg0620312022	C -> T	LOC_Os06g34930.1	downstream_gene_variant ; 2539.0bp to feature; MODIFIER	silent_mutation	Average:6.719; most accessible tissue: Callus, score: 17.666	N	N	N	N
vg0620312022	C -> T	LOC_Os06g34920-LOC_Os06g34930	intergenic_region ; MODIFIER	silent_mutation	Average:6.719; most accessible tissue: Callus, score: 17.666	N	N	N	N
vg0620312022	C -> DEL	N	N	silent_mutation	Average:6.719; most accessible tissue: Callus, score: 17.666	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0620312022	3.66E-07	9.63E-11	mr1238	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
vg0620312022	3.29E-06	1.32E-08	mr1309	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
vg0620312022	3.00E-08	9.52E-13	mr1841	Ind_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
vg0620312022	8.73E-10	8.72E-10	mr1900	Ind_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
vg0620312022	8.08E-06	8.98E-09	mr1238_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
vg0620312022	4.11E-06	1.17E-08	mr1484_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
vg0620312022	NA	1.65E-09	mr1841_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
vg0620312022	NA	8.82E-08	mr1900_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