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Detailed information for vg0709175210:

Variant ID: vg0709175210 (JBrowse)	Variation Type: SNP
Chromosome: chr07	Position: 9175210
Reference Allele: T	Alternative Allele: C
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, others allele: 0.00, population size: 115. )

Flanking Sequence (100 bp) in Reference Genome:

CTGGATTACCCTGGAGGAGACGGTGAGACGCATCTACGAGACACAAGCCAAGCCATTATTCTATGGCGCAGGCGGTACATCATCCTCCCTGGGCAACAAG[T/C]
GGCGTCTCGTGCACCATCTCCTCCGGCTCCGCCATCTCCTCCTCAGGATCCTGCACCGTCTCCTCCTCATGCTCCAGCACCGTCTCCACCTCAGGCTCCT

Reverse complement sequence

AGGAGCCTGAGGTGGAGACGGTGCTGGAGCATGAGGAGGAGACGGTGCAGGATCCTGAGGAGGAGATGGCGGAGCCGGAGGAGATGGTGCACGAGACGCC[A/G]
CTTGTTGCCCAGGGAGGATGATGTACCGCCTGCGCCATAGAATAATGGCTTGGCTTGTGTCTCGTAGATGCGTCTCACCGTCTCCTCCAGGGTAATCCAG

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	41.00%	4.70%	18.62%	35.67%	NA
All Indica	2759	13.40%	0.10%	28.31%	58.21%	NA
All Japonica	1512	80.00%	14.30%	3.64%	2.12%	NA
Aus	269	88.80%	0.00%	5.20%	5.95%	NA
Indica I	595	9.10%	0.00%	44.37%	46.55%	NA
Indica II	465	12.30%	0.00%	18.49%	69.25%	NA
Indica III	913	12.70%	0.00%	26.07%	61.23%	NA
Indica Intermediate	786	18.20%	0.30%	24.55%	57.00%	NA
Temperate Japonica	767	73.00%	24.10%	0.39%	2.48%	NA
Tropical Japonica	504	88.10%	0.20%	9.72%	1.98%	NA
Japonica Intermediate	241	85.10%	12.40%	1.24%	1.24%	NA
VI/Aromatic	96	83.30%	2.10%	14.58%	0.00%	NA
Intermediate	90	45.60%	1.10%	17.78%	35.56%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0709175210	T -> DEL	LOC_Os07g15800.1	N	frameshift_variant	Average:13.902; most accessible tissue: Callus, score: 20.5	N	N	N	N
vg0709175210	T -> C	LOC_Os07g15800.1	missense_variant ; p.Val468Ala; MODERATE	nonsynonymous_codon ; V468A	Average:13.902; most accessible tissue: Callus, score: 20.5	unknown	unknown	TOLERATED	1.00

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0709175210	NA	3.62E-06	mr1038	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
vg0709175210	NA	2.35E-11	mr1316	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
vg0709175210	NA	1.68E-10	mr1325	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
vg0709175210	NA	7.03E-06	mr1363	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
vg0709175210	NA	9.97E-07	mr1389	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
vg0709175210	2.30E-06	2.30E-06	mr1527	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
vg0709175210	NA	3.47E-06	mr1532	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
vg0709175210	NA	1.83E-06	mr1553	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
vg0709175210	NA	8.19E-08	mr1648	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
vg0709175210	4.92E-07	4.92E-07	mr1893	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
vg0709175210	2.19E-06	3.03E-09	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
vg0709175210	7.18E-06	4.43E-06	mr1293_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
vg0709175210	NA	1.20E-07	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
vg0709175210	NA	2.30E-07	mr1527_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
vg0709175210	NA	7.20E-07	mr1653_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
vg0709175210	NA	7.66E-06	mr1682_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
vg0709175210	NA	1.04E-06	mr1875_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