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Detailed information for vg0103143509:

Variant ID: vg0103143509 (JBrowse)	Variation Type: SNP
Chromosome: chr01	Position: 3143509
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

CAACATACAAGAACCTGAAAGCATCACTACAGCTTCACTATAGTTTTAGAGCAATTTTACGGTACTTGAGGAGATACCATGAGGTACCATTTTTTCTATT[G/A]
TAAATTTGGTACCTCTTGGTACCTAGGTACTATGAGGTACTAAAATTTTGGTACCTCATGATACCTCCTTAAGAACCGTAGAATTGCTCATAGTTTTAAC

Reverse complement sequence

GTTAAAACTATGAGCAATTCTACGGTTCTTAAGGAGGTATCATGAGGTACCAAAATTTTAGTACCTCATAGTACCTAGGTACCAAGAGGTACCAAATTTA[C/T]
AATAGAAAAAATGGTACCTCATGGTATCTCCTCAAGTACCGTAAAATTGCTCTAAAACTATAGTGAAGCTGTAGTGATGCTTTCAGGTTCTTGTATGTTG

Allele Frequencies:

Populations	Population Size	Frequency of G(primary allele)	Frequency of A(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	27.20%	0.40%	0.68%	71.67%	NA
All Indica	2759	7.30%	0.10%	0.87%	91.66%	NA
All Japonica	1512	48.00%	0.00%	0.33%	51.65%	NA
Aus	269	86.60%	6.30%	0.00%	7.06%	NA
Indica I	595	4.40%	0.20%	0.84%	94.62%	NA
Indica II	465	8.40%	0.00%	0.86%	90.75%	NA
Indica III	913	9.20%	0.10%	0.77%	89.92%	NA
Indica Intermediate	786	6.70%	0.30%	1.02%	91.98%	NA
Temperate Japonica	767	76.40%	0.00%	0.13%	23.47%	NA
Tropical Japonica	504	5.80%	0.00%	0.40%	93.85%	NA
Japonica Intermediate	241	46.10%	0.00%	0.83%	53.11%	NA
VI/Aromatic	96	95.80%	0.00%	0.00%	4.17%	NA
Intermediate	90	36.70%	0.00%	3.33%	60.00%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0103143509	G -> A	LOC_Os01g06660.1	upstream_gene_variant ; 3292.0bp to feature; MODIFIER	silent_mutation	Average:12.847; most accessible tissue: Callus, score: 74.613	N	N	N	N
vg0103143509	G -> A	LOC_Os01g06670.1	downstream_gene_variant ; 92.0bp to feature; MODIFIER	silent_mutation	Average:12.847; most accessible tissue: Callus, score: 74.613	N	N	N	N
vg0103143509	G -> A	LOC_Os01g06680.1	downstream_gene_variant ; 3870.0bp to feature; MODIFIER	silent_mutation	Average:12.847; most accessible tissue: Callus, score: 74.613	N	N	N	N
vg0103143509	G -> A	LOC_Os01g06660-LOC_Os01g06670	intergenic_region ; MODIFIER	silent_mutation	Average:12.847; most accessible tissue: Callus, score: 74.613	N	N	N	N
vg0103143509	G -> DEL	N	N	silent_mutation	Average:12.847; most accessible tissue: Callus, score: 74.613	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0103143509	1.65E-06	NA	mr1030	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
vg0103143509	6.62E-06	NA	mr1045	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
vg0103143509	8.68E-06	NA	mr1046	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
vg0103143509	1.69E-06	NA	mr1054	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
vg0103143509	7.64E-06	NA	mr1060	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
vg0103143509	NA	8.22E-10	mr1151	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
vg0103143509	3.71E-06	NA	mr1157	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
vg0103143509	1.80E-06	7.83E-19	mr1164	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
vg0103143509	4.61E-07	1.04E-08	mr1215	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
vg0103143509	NA	9.77E-14	mr1218	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
vg0103143509	NA	7.63E-08	mr1220	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
vg0103143509	2.56E-07	NA	mr1230	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
vg0103143509	NA	1.99E-09	mr1249	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
vg0103143509	3.58E-07	NA	mr1287	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
vg0103143509	8.23E-06	NA	mr1290	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
vg0103143509	2.06E-07	NA	mr1314	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
vg0103143509	NA	7.09E-07	mr1315	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
vg0103143509	3.18E-06	NA	mr1323	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
vg0103143509	1.31E-07	NA	mr1327	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
vg0103143509	6.15E-06	6.15E-06	mr1327	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
vg0103143509	NA	5.84E-07	mr1338	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
vg0103143509	2.02E-06	1.03E-12	mr1352	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
vg0103143509	3.16E-06	NA	mr1359	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
vg0103143509	1.05E-06	NA	mr1372	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
vg0103143509	8.51E-06	NA	mr1442	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
vg0103143509	4.97E-06	NA	mr1446	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
vg0103143509	5.84E-06	3.54E-08	mr1450	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
vg0103143509	4.39E-07	NA	mr1472	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
vg0103143509	NA	6.62E-08	mr1488	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
vg0103143509	NA	4.53E-07	mr1511	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
vg0103143509	9.45E-06	1.28E-10	mr1575	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
vg0103143509	NA	1.36E-16	mr1583	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
vg0103143509	NA	7.25E-08	mr1604	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
vg0103143509	1.51E-06	NA	mr1614	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
vg0103143509	NA	2.77E-07	mr1622	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
vg0103143509	NA	7.61E-07	mr1781	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
vg0103143509	3.03E-06	NA	mr1809	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
vg0103143509	6.39E-06	2.30E-07	mr1810	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
vg0103143509	5.11E-06	NA	mr1866	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
vg0103143509	NA	1.19E-08	mr1881	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
vg0103143509	NA	9.72E-07	mr1886	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
vg0103143509	2.16E-07	2.16E-07	mr1967	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
vg0103143509	NA	2.56E-22	mr1401_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