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Detailed information for vg0724424690:

Variant ID: vg0724424690 (JBrowse)	Variation Type: SNP
Chromosome: chr07	Position: 24424690
Reference Allele: T	Alternative Allele: C
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.59, C: 0.41, others allele: 0.00, population size: 88. )

Flanking Sequence (100 bp) in Reference Genome:

TCTTGGAGAAGACTAGCATCGGACCGACCGCCGCTAAGCTAACAACGGAAACAACCAAGATCGCCCAAAACCCTATCCTTACAAACAACATAAAGCCCAA[T/C]
TCATCCACGTCTTCAGGATCTAGGGAGAAAGGGTGGGAGAGAAGATGGAACACCTCTCCCCCTAGGCCCTCCGCCGTGGCCAACTTGTTGAAACTAGGAC

Reverse complement sequence

GTCCTAGTTTCAACAAGTTGGCCACGGCGGAGGGCCTAGGGGGAGAGGTGTTCCATCTTCTCTCCCACCCTTTCTCCCTAGATCCTGAAGACGTGGATGA[A/G]
TTGGGCTTTATGTTGTTTGTAAGGATAGGGTTTTGGGCGATCTTGGTTGTTTCCGTTGTTAGCTTAGCGGCGGTCGGTCCGATGCTAGTCTTCTCCAAGA

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	88.50%	11.50%	0.02%	0.00%	NA
All Indica	2759	98.50%	1.40%	0.04%	0.00%	NA
All Japonica	1512	67.50%	32.50%	0.00%	0.00%	NA
Aus	269	100.00%	0.00%	0.00%	0.00%	NA
Indica I	595	98.30%	1.70%	0.00%	0.00%	NA
Indica II	465	98.50%	1.50%	0.00%	0.00%	NA
Indica III	913	99.90%	0.10%	0.00%	0.00%	NA
Indica Intermediate	786	97.10%	2.80%	0.13%	0.00%	NA
Temperate Japonica	767	40.00%	60.00%	0.00%	0.00%	NA
Tropical Japonica	504	99.40%	0.60%	0.00%	0.00%	NA
Japonica Intermediate	241	88.00%	12.00%	0.00%	0.00%	NA
VI/Aromatic	96	97.90%	2.10%	0.00%	0.00%	NA
Intermediate	90	88.90%	11.10%	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
vg0724424690	T -> C	LOC_Os07g40750.1	upstream_gene_variant ; 2358.0bp to feature; MODIFIER	silent_mutation	Average:51.659; most accessible tissue: Zhenshan97 panicle, score: 69.946	N	N	N	N
vg0724424690	T -> C	LOC_Os07g40770.1	downstream_gene_variant ; 4497.0bp to feature; MODIFIER	silent_mutation	Average:51.659; most accessible tissue: Zhenshan97 panicle, score: 69.946	N	N	N	N
vg0724424690	T -> C	LOC_Os07g40760.1	intron_variant ; MODIFIER	silent_mutation	Average:51.659; most accessible tissue: Zhenshan97 panicle, score: 69.946	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0724424690	NA	8.66E-10	mr1282	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
vg0724424690	1.88E-08	NA	mr1343	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
vg0724424690	1.03E-21	1.56E-14	mr1354	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
vg0724424690	9.92E-15	1.38E-08	mr1354	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
vg0724424690	4.53E-06	4.51E-06	mr1703	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
vg0724424690	6.85E-12	NA	mr1829	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
vg0724424690	3.82E-11	NA	mr1829	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
vg0724424690	5.06E-07	NA	mr1902	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
vg0724424690	4.24E-07	NA	mr1902	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
vg0724424690	6.47E-09	NA	mr1181_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
vg0724424690	2.24E-37	1.66E-16	mr1354_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
vg0724424690	4.55E-25	3.07E-08	mr1354_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
vg0724424690	NA	1.30E-07	mr1399_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
vg0724424690	8.51E-08	NA	mr1567_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
vg0724424690	1.52E-06	NA	mr1567_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
vg0724424690	1.62E-10	NA	mr1679_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
vg0724424690	1.64E-06	NA	mr1679_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
vg0724424690	7.00E-21	NA	mr1829_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
vg0724424690	1.05E-14	1.59E-07	mr1829_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
vg0724424690	1.39E-19	NA	mr1902_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
vg0724424690	6.12E-14	5.10E-06	mr1902_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