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Detailed information for vg1125990989:

Variant ID: vg1125990989 (JBrowse)	Variation Type: SNP
Chromosome: chr11	Position: 25990989
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: 127. )

Flanking Sequence (100 bp) in Reference Genome:

GCCTACCACTAGCGTCAACCTCTCTTATAACTTGCACTGTGGTCGGCCATATATTTTGTGACCGGGGATTTGTACTAGACCTACTTGCACTTGTCCCGCC[C/T]
GACATCGACGTATGTTGTTCCTGCGGCAATTCTGCAGCACAAACAGAAGGCAATATTTGCTAAGGGGTGCTAGCTAAAATTTATGTGGTCATGTGGTGAA

Reverse complement sequence

TTCACCACATGACCACATAAATTTTAGCTAGCACCCCTTAGCAAATATTGCCTTCTGTTTGTGCTGCAGAATTGCCGCAGGAACAACATACGTCGATGTC[G/A]
GGCGGGACAAGTGCAAGTAGGTCTAGTACAAATCCCCGGTCACAAAATATATGGCCGACCACAGTGCAAGTTATAAGAGAGGTTGACGCTAGTGGTAGGC

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	93.00%	4.50%	1.23%	1.31%	NA
All Indica	2759	88.30%	7.40%	2.10%	2.21%	NA
All Japonica	1512	99.80%	0.20%	0.00%	0.00%	NA
Aus	269	98.50%	1.50%	0.00%	0.00%	NA
Indica I	595	100.00%	0.00%	0.00%	0.00%	NA
Indica II	465	82.40%	17.20%	0.22%	0.22%	NA
Indica III	913	82.10%	6.50%	5.59%	5.81%	NA
Indica Intermediate	786	90.20%	8.10%	0.76%	0.89%	NA
Temperate Japonica	767	99.60%	0.40%	0.00%	0.00%	NA
Tropical Japonica	504	100.00%	0.00%	0.00%	0.00%	NA
Japonica Intermediate	241	100.00%	0.00%	0.00%	0.00%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	97.80%	1.10%	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
vg1125990989	C -> T	LOC_Os11g43080.1	synonymous_variant ; p.Ser20Ser; LOW	synonymous_codon	Average:33.469; most accessible tissue: Zhenshan97 flag leaf, score: 59.429	N	N	N	N
vg1125990989	C -> DEL	LOC_Os11g43080.1	N	frameshift_variant	Average:33.469; most accessible tissue: Zhenshan97 flag leaf, score: 59.429	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1125990989	3.98E-14	3.42E-15	mr1238	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
vg1125990989	3.80E-07	8.11E-08	mr1309	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
vg1125990989	3.18E-07	2.49E-08	mr1484	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
vg1125990989	3.65E-08	1.33E-08	mr1841	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
vg1125990989	4.85E-06	4.85E-06	mr1900	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
vg1125990989	7.44E-11	2.02E-12	mr1238_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
vg1125990989	4.86E-10	4.85E-12	mr1484_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
vg1125990989	2.15E-11	4.55E-12	mr1841_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
vg1125990989	9.29E-08	4.48E-09	mr1900_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
vg1125990989	1.34E-09	1.34E-09	mr1945_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