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Detailed information for vg1218153472:

Variant ID: vg1218153472 (JBrowse)	Variation Type: SNP
Chromosome: chr12	Position: 18153472
Reference Allele: T	Alternative Allele: C
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 1.00, others allele: 0.00, population size: 81. )

Flanking Sequence (100 bp) in Reference Genome:

TACGTCTCGCCGCTGCCCGGCTCTGTGCCACTAGAACTGCTGCTGCTATGGTCGCGGCTGCCACTAGGAGTAGCAGGTAACCAACCTCCGTTGCCACCGG[T/C]
TGGCCCCCTGACGGCTGACGCTGGAGCGAAGGAGAGAGCGGATGCGGGAGCTGACACTGGAGCAGGAGCTGGGGCTGGAGCTAGAGCTGCGGGCACTGCA

Reverse complement sequence

TGCAGTGCCCGCAGCTCTAGCTCCAGCCCCAGCTCCTGCTCCAGTGTCAGCTCCCGCATCCGCTCTCTCCTTCGCTCCAGCGTCAGCCGTCAGGGGGCCA[A/G]
CCGGTGGCAACGGAGGTTGGTTACCTGCTACTCCTAGTGGCAGCCGCGACCATAGCAGCAGCAGTTCTAGTGGCACAGAGCCGGGCAGCGGCGAGACGTA

Allele Frequencies:

Populations	Population Size	Frequency of T(primary allele)	Frequency of C(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	37.30%	36.80%	1.90%	23.99%	NA
All Indica	2759	5.40%	54.20%	3.23%	37.11%	NA
All Japonica	1512	90.70%	8.90%	0.00%	0.33%	NA
Aus	269	35.70%	31.20%	0.00%	33.09%	NA
Indica I	595	6.10%	86.90%	0.00%	7.06%	NA
Indica II	465	3.20%	49.50%	1.72%	45.59%	NA
Indica III	913	2.70%	40.10%	6.68%	50.49%	NA
Indica Intermediate	786	9.40%	48.70%	2.54%	39.31%	NA
Temperate Japonica	767	98.40%	1.00%	0.00%	0.52%	NA
Tropical Japonica	504	79.40%	20.60%	0.00%	0.00%	NA
Japonica Intermediate	241	90.00%	9.50%	0.00%	0.41%	NA
VI/Aromatic	96	83.30%	8.30%	0.00%	8.33%	NA
Intermediate	90	71.10%	18.90%	1.11%	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
vg1218153472	T -> C	LOC_Os12g30260.1	missense_variant ; p.Thr290Ala; MODERATE	nonsynonymous_codon ; T290V	Average:52.193; most accessible tissue: Minghui63 young leaf, score: 69.4	benign	-0.118	TOLERATED	0.05
vg1218153472	T -> C	LOC_Os12g30260.1	missense_variant ; p.Thr290Ala; MODERATE	nonsynonymous_codon ; T290A	Average:52.193; most accessible tissue: Minghui63 young leaf, score: 69.4	possibly damaging	-1.571	TOLERATED	1.00
vg1218153472	T -> DEL	LOC_Os12g30260.1	N	frameshift_variant	Average:52.193; most accessible tissue: Minghui63 young leaf, score: 69.4	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1218153472	3.62E-06	2.64E-07	mr1170	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
vg1218153472	NA	1.59E-06	mr1864	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