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Detailed information for vg1118023819:

Variant ID: vg1118023819 (JBrowse)	Variation Type: SNP
Chromosome: chr11	Position: 18023819
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, others allele: 0.00, population size: 92. )

Flanking Sequence (100 bp) in Reference Genome:

GGCGCCGGACTCCCAGCGCTTTCGCCTTTCTTAGGCCCAGGAGAACGGCTTCGTATTCTGCTGCATTGTTGGTTGTGTCGAATTGTAATCTCGCTGCGTA[C/T]
CGAATCGGCACACCATTCGGCGAAAAGAGGACTGCTGCAACGCCTGCCCCCTTGTGCGACCACTAACCGTCAGAGCACATCACCCAGAACTGGTCGTCGG

Reverse complement sequence

CCGACGACCAGTTCTGGGTGATGTGCTCTGACGGTTAGTGGTCGCACAAGGGGGCAGGCGTTGCAGCAGTCCTCTTTTCGCCGAATGGTGTGCCGATTCG[G/A]
TACGCAGCGAGATTACAATTCGACACAACCAACAATGCAGCAGAATACGAAGCCGTTCTCCTGGGCCTAAGAAAGGCGAAAGCGCTGGGAGTCCGGCGCC

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	39.70%	0.10%	46.09%	14.07%	NA
All Indica	2759	23.10%	0.10%	59.15%	17.62%	NA
All Japonica	1512	70.80%	0.00%	21.43%	7.74%	NA
Aus	269	25.70%	0.40%	66.91%	7.06%	NA
Indica I	595	32.60%	0.30%	36.81%	30.25%	NA
Indica II	465	29.50%	0.20%	56.99%	13.33%	NA
Indica III	913	12.60%	0.00%	74.26%	13.14%	NA
Indica Intermediate	786	24.30%	0.10%	59.80%	15.78%	NA
Temperate Japonica	767	94.30%	0.00%	4.04%	1.69%	NA
Tropical Japonica	504	49.00%	0.00%	40.28%	10.71%	NA
Japonica Intermediate	241	41.90%	0.00%	37.34%	20.75%	NA
VI/Aromatic	96	59.40%	0.00%	8.33%	32.29%	NA
Intermediate	90	48.90%	0.00%	37.78%	13.33%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1118023819	C -> T	LOC_Os11g30990.1	splice_region_variant&intron_variant ; LOW	silent_mutation	Average:12.313; most accessible tissue: Zhenshan97 panicle, score: 16.188	N	N	N	N
vg1118023819	C -> T	LOC_Os11g30980.1	upstream_gene_variant ; 1024.0bp to feature; MODIFIER	silent_mutation	Average:12.313; most accessible tissue: Zhenshan97 panicle, score: 16.188	N	N	N	N
vg1118023819	C -> T	LOC_Os11g30970.1	downstream_gene_variant ; 3097.0bp to feature; MODIFIER	silent_mutation	Average:12.313; most accessible tissue: Zhenshan97 panicle, score: 16.188	N	N	N	N
vg1118023819	C -> DEL	N	N	silent_mutation	Average:12.313; most accessible tissue: Zhenshan97 panicle, score: 16.188	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1118023819	7.18E-06	7.18E-06	mr1929	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
vg1118023819	NA	3.07E-09	mr1042_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
vg1118023819	9.18E-06	9.18E-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
vg1118023819	NA	2.76E-08	mr1502_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
vg1118023819	NA	4.43E-06	mr1621_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
vg1118023819	NA	9.39E-06	mr1665_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
vg1118023819	NA	5.06E-08	mr1680_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
vg1118023819	NA	7.40E-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
vg1118023819	NA	6.01E-10	mr1871_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
vg1118023819	NA	3.46E-09	mr1929_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