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Detailed information for vg1222743479:

Variant ID: vg1222743479 (JBrowse)	Variation Type: SNP
Chromosome: chr12	Position: 22743479
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: 286. )

Flanking Sequence (100 bp) in Reference Genome:

CCACAGGGGCCGTGTTCGTCAATTCTCCCTCAGCTGGACATTGGACTACAACCACTTCTTCATCGTCGATTACTTGCTTGGATCCCCTCAGCTCTGCAAA[C/T]
TCCAGGAGTTTGAACTGTTCTATTTTAATATTGACGCTCAAAATCTGTGGTTCCGCTGTCTGTATTCTGTCTAGCGCATACTCTATGTGTTCTTAGGATT

Reverse complement sequence

AATCCTAAGAACACATAGAGTATGCGCTAGACAGAATACAGACAGCGGAACCACAGATTTTGAGCGTCAATATTAAAATAGAACAGTTCAAACTCCTGGA[G/A]
TTTGCAGAGCTGAGGGGATCCAAGCAAGTAATCGACGATGAAGAAGTGGTTGTAGTCCAATGTCCAGCTGAGGGAGAATTGACGAACACGGCCCCTGTGG

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	83.90%	0.40%	1.67%	14.05%	NA
All Indica	2759	72.80%	0.60%	2.83%	23.81%	NA
All Japonica	1512	99.70%	0.10%	0.07%	0.13%	NA
Aus	269	100.00%	0.00%	0.00%	0.00%	NA
Indica I	595	89.20%	0.30%	2.18%	8.24%	NA
Indica II	465	80.00%	0.90%	1.08%	18.06%	NA
Indica III	913	56.30%	0.50%	4.05%	39.10%	NA
Indica Intermediate	786	75.20%	0.60%	2.93%	21.25%	NA
Temperate Japonica	767	100.00%	0.00%	0.00%	0.00%	NA
Tropical Japonica	504	99.20%	0.20%	0.20%	0.40%	NA
Japonica Intermediate	241	100.00%	0.00%	0.00%	0.00%	NA
VI/Aromatic	96	99.00%	0.00%	0.00%	1.04%	NA
Intermediate	90	95.60%	0.00%	0.00%	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
vg1222743479	C -> DEL	LOC_Os12g37120.1	N	frameshift_variant	Average:72.868; most accessible tissue: Zhenshan97 young leaf, score: 87.004	N	N	N	N
vg1222743479	C -> T	LOC_Os12g37120.1	missense_variant ; p.Leu48Phe; MODERATE	nonsynonymous_codon ; L48F	Average:72.868; most accessible tissue: Zhenshan97 young leaf, score: 87.004	unknown	unknown	DELETERIOUS	0.00

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1222743479	6.45E-07	5.77E-07	mr1310_2	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