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Detailed information for vg1205231921:

Variant ID: vg1205231921 (JBrowse)	Variation Type: SNP
Chromosome: chr12	Position: 5231921
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, others allele: 0.00, population size: 49. )

Flanking Sequence (100 bp) in Reference Genome:

AGAAGATGGAGCACTGGACCATGCATTTTGACGGATCAAAACGACTTTCGGGTACTGGAGCAGGAGTGGTTTTAATTTCCCTAACTGGAGAAAGATTAAG[C/T]
TATGTGCTTTGGATACATTTTTCGGCATCCCACAACGTCGCCGAGTATGAGGCGCTCCTTCATGGACTGAGGATTGCGATTTCCCTAGGGATAAAGCGTC

Reverse complement sequence

GACGCTTTATCCCTAGGGAAATCGCAATCCTCAGTCCATGAAGGAGCGCCTCATACTCGGCGACGTTGTGGGATGCCGAAAAATGTATCCAAAGCACATA[G/A]
CTTAATCTTTCTCCAGTTAGGGAAATTAAAACCACTCCTGCTCCAGTACCCGAAAGTCGTTTTGATCCGTCAAAATGCATGGTCCAGTGCTCCATCTTCT

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	71.20%	3.00%	15.87%	9.94%	NA
All Indica	2759	54.00%	5.00%	25.88%	15.15%	NA
All Japonica	1512	99.70%	0.10%	0.00%	0.26%	NA
Aus	269	72.10%	0.70%	10.78%	16.36%	NA
Indica I	595	72.10%	0.50%	17.14%	10.25%	NA
Indica II	465	46.90%	16.10%	20.43%	16.56%	NA
Indica III	913	41.20%	1.50%	37.79%	19.50%	NA
Indica Intermediate	786	59.30%	5.90%	21.88%	12.98%	NA
Temperate Japonica	767	99.50%	0.00%	0.00%	0.52%	NA
Tropical Japonica	504	99.80%	0.20%	0.00%	0.00%	NA
Japonica Intermediate	241	100.00%	0.00%	0.00%	0.00%	NA
VI/Aromatic	96	97.90%	0.00%	2.08%	0.00%	NA
Intermediate	90	87.80%	2.20%	5.56%	4.44%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1205231921	C -> DEL	LOC_Os12g09860.1	N	frameshift_variant	Average:11.953; most accessible tissue: Zhenshan97 panicle, score: 20.424	N	N	N	N
vg1205231921	C -> T	LOC_Os12g09860.1	synonymous_variant ; p.Ser1471Ser; LOW	synonymous_codon	Average:11.953; most accessible tissue: Zhenshan97 panicle, score: 20.424	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1205231921	NA	7.43E-06	mr1122	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
vg1205231921	3.95E-08	3.16E-14	mr1889	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
vg1205231921	4.13E-07	NA	mr1896	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
vg1205231921	3.16E-08	1.21E-13	mr1896	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
vg1205231921	NA	4.13E-11	mr1903	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
vg1205231921	4.16E-08	NA	mr1907	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
vg1205231921	1.02E-09	3.20E-17	mr1907	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
vg1205231921	3.21E-06	3.21E-06	mr1926	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
vg1205231921	5.02E-06	NA	mr1934	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
vg1205231921	1.55E-06	1.04E-13	mr1934	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
vg1205231921	4.36E-08	NA	mr1935	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
vg1205231921	8.23E-07	2.14E-11	mr1935	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
vg1205231921	NA	2.21E-07	mr1896_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