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Detailed information for vg1221513464:

Variant ID: vg1221513464 (JBrowse)	Variation Type: SNP
Chromosome: chr12	Position: 21513464
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: 100. )

Flanking Sequence (100 bp) in Reference Genome:

AATACATTGCAACATATACTAAGGACACTAATGAATCTATCGCAGGAACCCACATCGTGTACCCTAGTCGTTAGGGTGACACCAGGATTTGCAATTCCTG[C/T]
CGTAGAGGGTCAAGCGTTCAAGTCTACCCTGGAGACCCGAGTGCATGGGGCGCAGTTGCTAGCCGGCAATGCCAAAGTTCAGGTGGACTTAGTGAAGCCC

Reverse complement sequence

GGGCTTCACTAAGTCCACCTGAACTTTGGCATTGCCGGCTAGCAACTGCGCCCCATGCACTCGGGTCTCCAGGGTAGACTTGAACGCTTGACCCTCTACG[G/A]
CAGGAATTGCAAATCCTGGTGTCACCCTAACGACTAGGGTACACGATGTGGGTTCCTGCGATAGATTCATTAGTGTCCTTAGTATATGTTGCAATGTATT

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	93.10%	6.10%	0.21%	0.63%	NA
All Indica	2759	95.30%	3.50%	0.14%	1.09%	NA
All Japonica	1512	93.10%	6.50%	0.33%	0.00%	NA
Aus	269	90.00%	9.70%	0.37%	0.00%	NA
Indica I	595	100.00%	0.00%	0.00%	0.00%	NA
Indica II	465	89.70%	9.90%	0.43%	0.00%	NA
Indica III	913	94.60%	3.60%	0.00%	1.75%	NA
Indica Intermediate	786	95.70%	2.30%	0.25%	1.78%	NA
Temperate Japonica	767	100.00%	0.00%	0.00%	0.00%	NA
Tropical Japonica	504	81.00%	18.30%	0.79%	0.00%	NA
Japonica Intermediate	241	96.70%	2.90%	0.41%	0.00%	NA
VI/Aromatic	96	46.90%	53.10%	0.00%	0.00%	NA
Intermediate	90	85.60%	14.40%	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
vg1221513464	C -> DEL	LOC_Os12g35380.1	N	frameshift_variant	Average:63.127; most accessible tissue: Zhenshan97 flag leaf, score: 75.761	N	N	N	N
vg1221513464	C -> T	LOC_Os12g35380.1	missense_variant ; p.Ala272Val; MODERATE	nonsynonymous_codon ; A272V	Average:63.127; most accessible tissue: Zhenshan97 flag leaf, score: 75.761	unknown	unknown	TOLERATED	0.33

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1221513464	NA	5.34E-06	mr1262	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
vg1221513464	1.62E-07	1.62E-07	mr1266	Jap_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
vg1221513464	NA	3.11E-06	mr1408	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
vg1221513464	NA	5.15E-06	mr1870_2	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