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Detailed information for vg1222478770:

Variant ID: vg1222478770 (JBrowse)	Variation Type: SNP
Chromosome: chr12	Position: 22478770
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.71, T: 0.29, others allele: 0.00, population size: 77. )

Flanking Sequence (100 bp) in Reference Genome:

AAGTAAGTATCCATCGGCTGGATCAAGCTTCGATTGATGAGCTCGCTGAAGTAGCTCTCTCCAATCTCCTGCAAGCTTGTCCCTGCAAGTCGTGTTTCAT[C/T]
TGTAATAAAACCCTCTGCTAACCAACCCCATATCAAAACATCTTTTCTAATTAGCTCATCCTCAGGATATTTGCTTAGAGACAACAAGCAAGTCTTCAAA

Reverse complement sequence

TTTGAAGACTTGCTTGTTGTCTCTAAGCAAATATCCTGAGGATGAGCTAATTAGAAAAGATGTTTTGATATGGGGTTGGTTAGCAGAGGGTTTTATTACA[G/A]
ATGAAACACGACTTGCAGGGACAAGCTTGCAGGAGATTGGAGAGAGCTACTTCAGCGAGCTCATCAATCGAAGCTTGATCCAGCCGATGGATACTTACTT

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	57.50%	22.90%	2.05%	17.54%	NA
All Indica	2759	40.80%	37.00%	3.08%	19.10%	NA
All Japonica	1512	87.40%	3.40%	0.20%	9.06%	NA
Aus	269	40.10%	0.00%	1.86%	57.99%	NA
Indica I	595	58.70%	27.10%	3.19%	11.09%	NA
Indica II	465	31.20%	47.50%	1.29%	20.00%	NA
Indica III	913	36.70%	33.30%	4.27%	25.74%	NA
Indica Intermediate	786	37.80%	42.60%	2.67%	16.92%	NA
Temperate Japonica	767	92.60%	4.20%	0.26%	3.00%	NA
Tropical Japonica	504	78.00%	1.00%	0.20%	20.83%	NA
Japonica Intermediate	241	90.50%	5.80%	0.00%	3.73%	NA
VI/Aromatic	96	96.90%	1.00%	1.04%	1.04%	NA
Intermediate	90	78.90%	8.90%	3.33%	8.89%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1222478770	C -> DEL	LOC_Os12g36690.1	N	frameshift_variant	Average:18.137; most accessible tissue: Callus, score: 44.261	N	N	N	N
vg1222478770	C -> T	LOC_Os12g36690.1	missense_variant ; p.Asp448Asn; MODERATE	nonsynonymous_codon ; D448N	Average:18.137; most accessible tissue: Callus, score: 44.261	unknown	unknown	TOLERATED	0.58

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1222478770	NA	5.08E-06	mr1013	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
vg1222478770	NA	1.19E-06	mr1031	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
vg1222478770	NA	9.05E-07	mr1056	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
vg1222478770	5.26E-07	NA	mr1389	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
vg1222478770	NA	4.28E-09	mr1608	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
vg1222478770	NA	4.50E-06	mr1024_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
vg1222478770	2.74E-09	NA	mr1038_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
vg1222478770	2.70E-07	NA	mr1038_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
vg1222478770	1.11E-07	NA	mr1389_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
vg1222478770	5.76E-06	NA	mr1389_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