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Detailed information for vg1125569375:

Variant ID: vg1125569375 (JBrowse)	Variation Type: SNP
Chromosome: chr11	Position: 25569375
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.98, T: 0.01, others allele: 0.00, population size: 245. )

Flanking Sequence (100 bp) in Reference Genome:

ATAAGCACACTACTACCCCTTATATTTCTTTTTGTTACACTTCGATAGCCATATGCTACATAGTGATAGTCATACGATAAACCAAAAAGATCTTGCTACA[C/T]
GGGAAAAAAATATTCGATGCTCCTGTCGTTTTCTGTCTGTTCTTTTTTTTTTCACACAAGCTGGAGCTTTGGCCAAACTGCAATGGGCTGGGCTAGCTTA

Reverse complement sequence

TAAGCTAGCCCAGCCCATTGCAGTTTGGCCAAAGCTCCAGCTTGTGTGAAAAAAAAAAGAACAGACAGAAAACGACAGGAGCATCGAATATTTTTTTCCC[G/A]
TGTAGCAAGATCTTTTTGGTTTATCGTATGACTATCACTATGTAGCATATGGCTATCGAAGTGTAACAAAAAGAAATATAAGGGGTAGTAGTGTGCTTAT

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	84.80%	11.60%	0.17%	3.45%	NA
All Indica	2759	79.30%	16.00%	0.25%	4.49%	NA
All Japonica	1512	98.50%	1.40%	0.00%	0.13%	NA
Aus	269	77.00%	9.30%	0.37%	13.38%	NA
Indica I	595	97.50%	2.40%	0.00%	0.17%	NA
Indica II	465	81.30%	17.80%	0.22%	0.65%	NA
Indica III	913	66.00%	21.10%	0.44%	12.38%	NA
Indica Intermediate	786	79.60%	19.20%	0.25%	0.89%	NA
Temperate Japonica	767	98.30%	1.70%	0.00%	0.00%	NA
Tropical Japonica	504	99.20%	0.40%	0.00%	0.40%	NA
Japonica Intermediate	241	97.50%	2.50%	0.00%	0.00%	NA
VI/Aromatic	96	44.80%	55.20%	0.00%	0.00%	NA
Intermediate	90	90.00%	8.90%	0.00%	1.11%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1125569375	C -> T	LOC_Os11g42450-LOC_Os11g42470	intergenic_region ; MODIFIER	silent_mutation	Average:54.553; most accessible tissue: Minghui63 root, score: 70.803	N	N	N	N
vg1125569375	C -> DEL	N	N	silent_mutation	Average:54.553; most accessible tissue: Minghui63 root, score: 70.803	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1125569375	5.97E-16	2.71E-18	mr1191	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
vg1125569375	1.25E-10	8.76E-11	mr1191	Ind_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
vg1125569375	1.40E-19	9.81E-25	mr1644	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
vg1125569375	5.44E-13	7.71E-14	mr1644	Ind_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
vg1125569375	NA	2.65E-08	mr1829	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
vg1125569375	NA	1.42E-06	mr1133_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
vg1125569375	5.81E-22	1.67E-20	mr1191_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
vg1125569375	1.62E-11	8.56E-11	mr1191_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
vg1125569375	NA	1.76E-08	mr1829_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