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Detailed information for vg1020531763:

Variant ID: vg1020531763 (JBrowse)	Variation Type: SNP
Chromosome: chr10	Position: 20531763
Reference Allele: T	Alternative Allele: G
Primary Allele: T	Secondary Allele: G

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

CGGAGCCCTTAGACCCGCAGTGCGAGAATTTCGAGGATCAAGCCCAAGATCTCGAGCAAGGCAAGTCACCTTTGATCATCTTGCACCTATAACTTAAATC[T/G]
AAGTATTTCTTTTCCGCAAATATTGCATGAATAGGATTAACACGAGTACTTCGGCCACGGCTTGCGAGATAGCCTACTGGCCCCAATCCTAATTGCTGCA

Reverse complement sequence

TGCAGCAATTAGGATTGGGGCCAGTAGGCTATCTCGCAAGCCGTGGCCGAAGTACTCGTGTTAATCCTATTCATGCAATATTTGCGGAAAAGAAATACTT[A/C]
GATTTAAGTTATAGGTGCAAGATGATCAAAGGTGACTTGCCTTGCTCGAGATCTTGGGCTTGATCCTCGAAATTCTCGCACTGCGGGTCTAAGGGCTCCG

Allele Frequencies:

Populations	Population Size	Frequency of T(primary allele)	Frequency of G(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	24.70%	9.50%	0.15%	65.68%	NA
All Indica	2759	2.20%	0.20%	0.22%	97.39%	NA
All Japonica	1512	62.60%	28.80%	0.07%	8.53%	NA
Aus	269	43.90%	0.00%	0.00%	56.13%	NA
Indica I	595	3.50%	0.00%	0.17%	96.30%	NA
Indica II	465	0.40%	0.90%	0.00%	98.71%	NA
Indica III	913	1.30%	0.00%	0.33%	98.36%	NA
Indica Intermediate	786	3.30%	0.10%	0.25%	96.31%	NA
Temperate Japonica	767	86.80%	11.10%	0.00%	2.09%	NA
Tropical Japonica	504	21.80%	58.70%	0.20%	19.25%	NA
Japonica Intermediate	241	70.50%	22.80%	0.00%	6.64%	NA
VI/Aromatic	96	11.50%	0.00%	0.00%	88.54%	NA
Intermediate	90	35.60%	6.70%	0.00%	57.78%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1020531763	T -> G	LOC_Os10g38420.1	downstream_gene_variant ; 2228.0bp to feature; MODIFIER	silent_mutation	Average:6.361; most accessible tissue: Callus, score: 14.153	N	N	N	N
vg1020531763	T -> G	LOC_Os10g38440.1	downstream_gene_variant ; 614.0bp to feature; MODIFIER	silent_mutation	Average:6.361; most accessible tissue: Callus, score: 14.153	N	N	N	N
vg1020531763	T -> G	LOC_Os10g38420-LOC_Os10g38440	intergenic_region ; MODIFIER	silent_mutation	Average:6.361; most accessible tissue: Callus, score: 14.153	N	N	N	N
vg1020531763	T -> DEL	N	N	silent_mutation	Average:6.361; most accessible tissue: Callus, score: 14.153	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1020531763	7.84E-06	NA	mr1076	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
vg1020531763	NA	8.72E-06	mr1076	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
vg1020531763	2.99E-06	NA	mr1226	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
vg1020531763	NA	2.64E-06	mr1226	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
vg1020531763	NA	2.65E-07	mr1408	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
vg1020531763	4.84E-06	NA	mr1159_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
vg1020531763	9.57E-06	9.57E-06	mr1159_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
vg1020531763	8.79E-06	2.05E-08	mr1184_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
vg1020531763	NA	6.60E-06	mr1267_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
vg1020531763	7.09E-07	4.49E-09	mr1278_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
vg1020531763	4.34E-06	4.34E-06	mr1278_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
vg1020531763	8.75E-07	4.17E-08	mr1284_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
vg1020531763	3.67E-06	3.67E-06	mr1284_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
vg1020531763	6.66E-07	6.65E-07	mr1286_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
vg1020531763	NA	4.86E-07	mr1293_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
vg1020531763	9.31E-06	9.31E-06	mr1293_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
vg1020531763	2.96E-06	2.95E-06	mr1311_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
vg1020531763	3.22E-07	8.55E-07	mr1312_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
vg1020531763	6.16E-06	6.16E-06	mr1312_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
vg1020531763	NA	2.99E-07	mr1329_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
vg1020531763	NA	4.85E-06	mr1337_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
vg1020531763	2.01E-06	3.43E-10	mr1369_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
vg1020531763	NA	2.87E-06	mr1373_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
vg1020531763	4.07E-06	4.06E-06	mr1373_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
vg1020531763	8.18E-08	3.45E-09	mr1374_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
vg1020531763	9.42E-07	9.41E-07	mr1374_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
vg1020531763	1.40E-07	1.06E-09	mr1397_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
vg1020531763	7.99E-06	5.25E-07	mr1397_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
vg1020531763	2.21E-06	1.53E-10	mr1453_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
vg1020531763	NA	1.28E-06	mr1467_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
vg1020531763	3.89E-06	7.61E-09	mr1524_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
vg1020531763	NA	9.63E-07	mr1556_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
vg1020531763	2.58E-06	2.81E-08	mr1652_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
vg1020531763	1.12E-07	8.12E-06	mr1663_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
vg1020531763	2.25E-06	2.25E-06	mr1663_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
vg1020531763	4.80E-07	1.77E-08	mr1665_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
vg1020531763	1.28E-07	1.28E-07	mr1674_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
vg1020531763	2.24E-06	2.24E-06	mr1674_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
vg1020531763	1.02E-06	4.65E-11	mr1683_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
vg1020531763	NA	5.08E-06	mr1683_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
vg1020531763	2.22E-06	1.85E-08	mr1687_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
vg1020531763	4.90E-07	4.91E-07	mr1688_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
vg1020531763	2.70E-06	2.70E-06	mr1688_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
vg1020531763	6.77E-06	3.87E-06	mr1738_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
vg1020531763	NA	6.61E-06	mr1738_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
vg1020531763	NA	1.52E-06	mr1764_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
vg1020531763	2.27E-07	2.27E-07	mr1766_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
vg1020531763	1.24E-06	5.17E-09	mr1812_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
vg1020531763	7.10E-06	2.37E-07	mr1812_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
vg1020531763	NA	7.49E-06	mr1816_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
vg1020531763	1.12E-06	1.18E-07	mr1832_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
vg1020531763	4.88E-07	4.88E-07	mr1832_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
vg1020531763	2.38E-07	2.18E-08	mr1833_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
vg1020531763	9.79E-07	8.21E-08	mr1833_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
vg1020531763	4.84E-07	6.20E-08	mr1843_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
vg1020531763	9.83E-08	9.82E-08	mr1843_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
vg1020531763	1.45E-07	1.45E-07	mr1847_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
vg1020531763	2.63E-07	2.63E-07	mr1847_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
vg1020531763	NA	8.51E-10	mr1851_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
vg1020531763	NA	3.82E-06	mr1984_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