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Detailed information for vg1226852502:

Variant ID: vg1226852502 (JBrowse)	Variation Type: SNP
Chromosome: chr12	Position: 26852502
Reference Allele: C	Alternative Allele: A
Primary Allele: A	Secondary Allele: C

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.87, A: 0.13, others allele: 0.00, population size: 94. )

Flanking Sequence (100 bp) in Reference Genome:

ACATATAAGAAACATATCTCTAATTGATGTCAATATACAACAAGAAAATGCATAGAAAAATTAAAAATATACGTACCATAATAAAGAAACCATCTTATAA[C/A]
TAGCCACTTGCTGTCATCCTACTCCCCTCCGTTCAATGCAAGCAACAAACACTAACTTAATCAATAATCATGGGTTATGGATAGTCTAGCAAAATTGAAA

Reverse complement sequence

TTTCAATTTTGCTAGACTATCCATAACCCATGATTATTGATTAAGTTAGTGTTTGTTGCTTGCATTGAACGGAGGGGAGTAGGATGACAGCAAGTGGCTA[G/T]
TTATAAGATGGTTTCTTTATTATGGTACGTATATTTTTAATTTTTCTATGCATTTTCTTGTTGTATATTGACATCAATTAGAGATATGTTTCTTATATGT

Allele Frequencies:

Populations	Population Size	Frequency of A(primary allele)	Frequency of C(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	51.50%	48.10%	0.28%	0.11%	NA
All Indica	2759	77.30%	22.10%	0.47%	0.18%	NA
All Japonica	1512	0.20%	99.80%	0.00%	0.00%	NA
Aus	269	91.10%	8.90%	0.00%	0.00%	NA
Indica I	595	34.50%	64.90%	0.67%	0.00%	NA
Indica II	465	92.00%	7.10%	0.43%	0.43%	NA
Indica III	913	92.20%	7.40%	0.22%	0.11%	NA
Indica Intermediate	786	83.60%	15.50%	0.64%	0.25%	NA
Temperate Japonica	767	0.00%	100.00%	0.00%	0.00%	NA
Tropical Japonica	504	0.20%	99.80%	0.00%	0.00%	NA
Japonica Intermediate	241	0.80%	99.20%	0.00%	0.00%	NA
VI/Aromatic	96	19.80%	80.20%	0.00%	0.00%	NA
Intermediate	90	38.90%	61.10%	0.00%	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
vg1226852502	C -> DEL	N	N	silent_mutation	Average:51.778; most accessible tissue: Zhenshan97 flag leaf, score: 71.238	N	N	N	N
vg1226852502	C -> A	LOC_Os12g43260.1	intron_variant ; MODIFIER	silent_mutation	Average:51.778; most accessible tissue: Zhenshan97 flag leaf, score: 71.238	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1226852502	NA	2.92E-06	mr1201	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
vg1226852502	4.25E-06	4.25E-06	mr1248	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
vg1226852502	NA	7.03E-08	mr1274	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
vg1226852502	NA	5.24E-11	mr1332	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
vg1226852502	NA	4.25E-06	mr1374	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
vg1226852502	NA	1.02E-07	mr1659	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
vg1226852502	NA	1.17E-19	mr1754	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
vg1226852502	NA	3.30E-13	mr1838_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