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Detailed information for vg0613294536:

Variant ID: vg0613294536 (JBrowse)	Variation Type: SNP
Chromosome: chr06	Position: 13294536
Reference Allele: C	Alternative Allele: T
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, others allele: 0.00, population size: 117. )

Flanking Sequence (100 bp) in Reference Genome:

TTTTTGTCTTGTTTTGAAGATAAATCGAGGATTCAACGAGATGACAAATCAGAAAATATGTCACTTCATTCATGTGGTTTTAATGAAATACCCCTCACTA[C/T]
AATACATTCACTAAAGCATCATTTAGTACGTTACCTTCCTATTAAAATACTACTTTAAAGAGCTTTAACAATTTTATAACCAAAACACTCCTACCTATAA

Reverse complement sequence

TTATAGGTAGGAGTGTTTTGGTTATAAAATTGTTAAAGCTCTTTAAAGTAGTATTTTAATAGGAAGGTAACGTACTAAATGATGCTTTAGTGAATGTATT[G/A]
TAGTGAGGGGTATTTCATTAAAACCACATGAATGAAGTGACATATTTTCTGATTTGTCATCTCGTTGAATCCTCGATTTATCTTCAAAACAAGACAAAAA

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	51.30%	44.80%	0.51%	3.43%	NA
All Indica	2759	78.60%	20.80%	0.40%	0.18%	NA
All Japonica	1512	4.30%	90.80%	0.20%	4.70%	NA
Aus	269	51.30%	15.60%	2.97%	30.11%	NA
Indica I	595	80.30%	19.30%	0.34%	0.00%	NA
Indica II	465	90.30%	9.20%	0.43%	0.00%	NA
Indica III	913	71.30%	28.10%	0.33%	0.22%	NA
Indica Intermediate	786	78.90%	20.20%	0.51%	0.38%	NA
Temperate Japonica	767	3.50%	96.50%	0.00%	0.00%	NA
Tropical Japonica	504	6.20%	81.20%	0.40%	12.30%	NA
Japonica Intermediate	241	2.90%	92.90%	0.41%	3.73%	NA
VI/Aromatic	96	13.50%	85.40%	1.04%	0.00%	NA
Intermediate	90	43.30%	50.00%	1.11%	5.56%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0613294536	C -> T	LOC_Os06g22810.1	upstream_gene_variant ; 2551.0bp to feature; MODIFIER	silent_mutation	Average:61.295; most accessible tissue: Zhenshan97 flower, score: 78.5	N	N	N	N
vg0613294536	C -> T	LOC_Os06g22800-LOC_Os06g22810	intergenic_region ; MODIFIER	silent_mutation	Average:61.295; most accessible tissue: Zhenshan97 flower, score: 78.5	N	N	N	N
vg0613294536	C -> DEL	N	N	silent_mutation	Average:61.295; most accessible tissue: Zhenshan97 flower, score: 78.5	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0613294536	1.68E-09	4.32E-15	mr1033	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
vg0613294536	6.24E-06	NA	mr1087	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
vg0613294536	NA	2.91E-08	mr1087	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
vg0613294536	NA	2.29E-06	mr1090	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
vg0613294536	3.44E-06	1.25E-09	mr1176	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
vg0613294536	1.03E-07	1.03E-07	mr1536	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
vg0613294536	NA	2.02E-08	mr1824	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
vg0613294536	1.04E-09	7.17E-19	mr1033_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
vg0613294536	2.38E-07	NA	mr1087_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
vg0613294536	NA	4.97E-11	mr1087_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
vg0613294536	NA	6.05E-09	mr1112_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
vg0613294536	NA	8.15E-11	mr1216_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
vg0613294536	1.99E-06	NA	mr1234_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
vg0613294536	9.98E-08	1.09E-09	mr1536_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