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Detailed information for vg1208143024:

Variant ID: vg1208143024 (JBrowse)	Variation Type: SNP
Chromosome: chr12	Position: 8143024
Reference Allele: G	Alternative Allele: A
Primary Allele: A	Secondary Allele: G

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.91, A: 0.09, others allele: 0.00, population size: 89. )

Flanking Sequence (100 bp) in Reference Genome:

CCGAGGACTAACTAGTTGGCCTGGTGCCGACGTAGACGCAGCAAGTGCGGGAGCCGATACCGGTGCCGTCGGCTGAGCTGATGGCGCATTGGGAGGAACT[G/A]
TTTGAACAGATGGCTGAGTATTGGTGATCAGAGGCCGATAATCTGGAAAGACACCTCCTTGCAAATAAACTGGGCCTGTAGCCTGATATTCAGCCATTGA

Reverse complement sequence

TCAATGGCTGAATATCAGGCTACAGGCCCAGTTTATTTGCAAGGAGGTGTCTTTCCAGATTATCGGCCTCTGATCACCAATACTCAGCCATCTGTTCAAA[C/T]
AGTTCCTCCCAATGCGCCATCAGCTCAGCCGACGGCACCGGTATCGGCTCCCGCACTTGCTGCGTCTACGTCGGCACCAGGCCAACTAGTTAGTCCTCGG

Allele Frequencies:

Populations	Population Size	Frequency of A(primary allele)	Frequency of G(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	27.00%	19.50%	0.83%	52.64%	NA
All Indica	2759	37.90%	7.40%	0.80%	53.82%	NA
All Japonica	1512	4.30%	43.50%	0.73%	51.46%	NA
Aus	269	30.50%	3.00%	1.86%	64.68%	NA
Indica I	595	48.60%	9.90%	0.84%	40.67%	NA
Indica II	465	52.30%	6.70%	0.22%	40.86%	NA
Indica III	913	25.60%	5.50%	0.77%	68.13%	NA
Indica Intermediate	786	35.80%	8.30%	1.15%	54.83%	NA
Temperate Japonica	767	6.30%	68.70%	0.65%	24.38%	NA
Tropical Japonica	504	1.80%	12.10%	0.60%	85.52%	NA
Japonica Intermediate	241	3.30%	29.00%	1.24%	66.39%	NA
VI/Aromatic	96	66.70%	20.80%	0.00%	12.50%	NA
Intermediate	90	20.00%	35.60%	1.11%	43.33%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1208143024	G -> DEL	LOC_Os12g14290.1	N	frameshift_variant	Average:37.197; most accessible tissue: Zhenshan97 flag leaf, score: 77.473	N	N	N	N
vg1208143024	G -> A	LOC_Os12g14290.1	missense_variant ; p.Thr226Ile; MODERATE	nonsynonymous_codon ; T226I	Average:37.197; most accessible tissue: Zhenshan97 flag leaf, score: 77.473	unknown	unknown	TOLERATED	0.33

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1208143024	NA	5.78E-07	mr1193	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
vg1208143024	NA	4.31E-10	mr1011_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
vg1208143024	NA	1.77E-06	mr1011_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
vg1208143024	1.36E-06	NA	mr1015_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
vg1208143024	2.67E-06	2.79E-08	mr1015_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
vg1208143024	NA	2.16E-14	mr1031_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
vg1208143024	NA	8.71E-07	mr1031_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
vg1208143024	NA	2.56E-06	mr1369_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
vg1208143024	NA	1.15E-06	mr1477_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
vg1208143024	NA	7.30E-09	mr1683_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