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Detailed information for vg0124266409:

Variant ID: vg0124266409 (JBrowse)	Variation Type: SNP
Chromosome: chr01	Position: 24266409
Reference Allele: T	Alternative Allele: C
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.01, others allele: 0.00, population size: 263. )

Flanking Sequence (100 bp) in Reference Genome:

CCAGTTCCCATCCTGACTACACCATTGATCGTGCGAGTGCTTCTTTCGTAACTCGACGACTCAACGATTGGGATTGGGGACCCGTGTCCAACGGGGGCAA[T/C]
CGGCGTCTGGCGACTAGGATCGAGAGCAGCGTTCAGCAAGCAGCTATGTCACTATGTCAGTTTCGGTTCGATTTTAGAAATTCCGATTAGAATTGGATTG

Reverse complement sequence

CAATCCAATTCTAATCGGAATTTCTAAAATCGAACCGAAACTGACATAGTGACATAGCTGCTTGCTGAACGCTGCTCTCGATCCTAGTCGCCAGACGCCG[A/G]
TTGCCCCCGTTGGACACGGGTCCCCAATCCCAATCGTTGAGTCGTCGAGTTACGAAAGAAGCACTCGCACGATCAATGGTGTAGTCAGGATGGGAACTGG

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	75.60%	24.00%	0.38%	0.00%	NA
All Indica	2759	99.70%	0.30%	0.00%	0.00%	NA
All Japonica	1512	27.20%	71.80%	0.99%	0.00%	NA
Aus	269	98.10%	1.90%	0.00%	0.00%	NA
Indica I	595	100.00%	0.00%	0.00%	0.00%	NA
Indica II	465	99.60%	0.40%	0.00%	0.00%	NA
Indica III	913	99.80%	0.20%	0.00%	0.00%	NA
Indica Intermediate	786	99.40%	0.60%	0.00%	0.00%	NA
Temperate Japonica	767	12.40%	86.20%	1.43%	0.00%	NA
Tropical Japonica	504	54.40%	44.80%	0.79%	0.00%	NA
Japonica Intermediate	241	17.80%	82.20%	0.00%	0.00%	NA
VI/Aromatic	96	89.60%	8.30%	2.08%	0.00%	NA
Intermediate	90	66.70%	32.20%	1.11%	0.00%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0124266409	T -> C	LOC_Os01g42660.1	synonymous_variant ; p.Asn82Asn; LOW	synonymous_codon	Average:48.576; most accessible tissue: Zhenshan97 panicle, score: 68.538	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0124266409	2.42E-08	2.28E-30	mr1238	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
vg0124266409	7.06E-07	8.40E-31	mr1309	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
vg0124266409	7.45E-08	4.72E-22	mr1484	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
vg0124266409	NA	6.14E-06	mr1484	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
vg0124266409	NA	9.51E-07	mr1622	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
vg0124266409	NA	3.72E-06	mr1837	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
vg0124266409	9.75E-07	1.82E-26	mr1841	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
vg0124266409	NA	4.28E-15	mr1900	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
vg0124266409	1.85E-06	2.11E-13	mr1945	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
vg0124266409	NA	1.69E-06	mr1227_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
vg0124266409	1.20E-06	1.34E-30	mr1238_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
vg0124266409	4.26E-06	3.66E-27	mr1484_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
vg0124266409	3.37E-07	1.18E-35	mr1841_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
vg0124266409	NA	2.81E-22	mr1900_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
vg0124266409	NA	9.31E-20	mr1945_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