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Detailed information for vg1000804159:

Variant ID: vg1000804159 (JBrowse)	Variation Type: SNP
Chromosome: chr10	Position: 804159
Reference Allele: T	Alternative Allele: C
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.68, C: 0.36, others allele: 0.00, population size: 28. )

Flanking Sequence (100 bp) in Reference Genome:

CAAAATTTAAAATTATGTTATCATTTTAATATATTTTAATAATAAATTGAGAAAACATATATGCTATTATATAAGAGAAAATATAATGATGCTAGCAGCG[T/C]
AATCTGCGGGGGCTAGAATGCTAGTTTAATATAAACGACGACCTTCACTAGAAATGGTAGTAGTGGCCTCTTGCACGGAATTTTTTTTTGAAAATAATAC

Reverse complement sequence

GTATTATTTTCAAAAAAAAATTCCGTGCAAGAGGCCACTACTACCATTTCTAGTGAAGGTCGTCGTTTATATTAAACTAGCATTCTAGCCCCCGCAGATT[A/G]
CGCTGCTAGCATCATTATATTTTCTCTTATATAATAGCATATATGTTTTCTCAATTTATTATTAAAATATATTAAAATGATAACATAATTTTAAATTTTG

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	35.10%	16.10%	0.11%	48.77%	NA
All Indica	2759	50.70%	0.70%	0.11%	48.53%	NA
All Japonica	1512	3.20%	47.80%	0.13%	48.81%	NA
Aus	269	37.20%	0.40%	0.00%	62.45%	NA
Indica I	595	63.00%	1.20%	0.00%	35.80%	NA
Indica II	465	24.50%	0.40%	0.43%	74.62%	NA
Indica III	913	51.00%	0.20%	0.11%	48.63%	NA
Indica Intermediate	786	56.40%	1.00%	0.00%	42.62%	NA
Temperate Japonica	767	0.90%	77.20%	0.00%	21.90%	NA
Tropical Japonica	504	3.40%	5.00%	0.20%	91.47%	NA
Japonica Intermediate	241	10.40%	44.00%	0.41%	45.23%	NA
VI/Aromatic	96	90.60%	0.00%	0.00%	9.38%	NA
Intermediate	90	25.60%	17.80%	0.00%	56.67%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1000804159	T -> C	LOC_Os10g02250.1	upstream_gene_variant ; 4791.0bp to feature; MODIFIER	silent_mutation	Average:22.708; most accessible tissue: Zhenshan97 panicle, score: 49.416	N	N	N	N
vg1000804159	T -> C	LOC_Os10g02260.1	downstream_gene_variant ; 1504.0bp to feature; MODIFIER	silent_mutation	Average:22.708; most accessible tissue: Zhenshan97 panicle, score: 49.416	N	N	N	N
vg1000804159	T -> C	LOC_Os10g02260.2	downstream_gene_variant ; 1510.0bp to feature; MODIFIER	silent_mutation	Average:22.708; most accessible tissue: Zhenshan97 panicle, score: 49.416	N	N	N	N
vg1000804159	T -> C	LOC_Os10g02250-LOC_Os10g02260	intergenic_region ; MODIFIER	silent_mutation	Average:22.708; most accessible tissue: Zhenshan97 panicle, score: 49.416	N	N	N	N
vg1000804159	T -> DEL	N	N	silent_mutation	Average:22.708; most accessible tissue: Zhenshan97 panicle, score: 49.416	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1000804159	2.69E-07	NA	mr1040_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
vg1000804159	NA	5.94E-06	mr1232_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
vg1000804159	8.64E-07	NA	mr1362_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
vg1000804159	4.65E-06	4.65E-06	mr1424_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
vg1000804159	3.69E-06	3.69E-06	mr1852_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
vg1000804159	NA	1.90E-06	mr1884_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
vg1000804159	7.92E-06	7.92E-06	mr1901_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
vg1000804159	NA	7.66E-06	mr1944_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