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Detailed information for vg0430989073:

Variant ID: vg0430989073 (JBrowse)	Variation Type: SNP
Chromosome: chr04	Position: 30989073
Reference Allele: T	Alternative Allele: C
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.99, others allele: 0.00, population size: 126. )

Flanking Sequence (100 bp) in Reference Genome:

TTATTTCAAAATAAGTTAATTTGTAATCCGTGATGTTTGTTAAAAATTAGTTGTGCAGTTTGGCGGTTTGATGCCCCTCTCTGCATTAAAGAACTTATAA[T/C]
TGCTGATTGTAATCTCCCTGGTTGAGAAATAAATTCACCCTTTCCCCGCAAAAAAAAATAACTTGTAATTTATAATACAAATGTAGAGAGTAGATAAAAA

Reverse complement sequence

TTTTTATCTACTCTCTACATTTGTATTATAAATTACAAGTTATTTTTTTTTGCGGGGAAAGGGTGAATTTATTTCTCAACCAGGGAGATTACAATCAGCA[A/G]
TTATAAGTTCTTTAATGCAGAGAGGGGCATCAAACCGCCAAACTGCACAACTAATTTTTAACAAACATCACGGATTACAAATTAACTTATTTTGAAATAA

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	69.80%	29.90%	0.28%	0.00%	NA
All Indica	2759	96.60%	3.20%	0.18%	0.00%	NA
All Japonica	1512	26.10%	73.60%	0.33%	0.00%	NA
Aus	269	34.90%	63.90%	1.12%	0.00%	NA
Indica I	595	98.00%	1.80%	0.17%	0.00%	NA
Indica II	465	92.70%	6.90%	0.43%	0.00%	NA
Indica III	913	98.10%	1.90%	0.00%	0.00%	NA
Indica Intermediate	786	96.20%	3.60%	0.25%	0.00%	NA
Temperate Japonica	767	42.10%	57.40%	0.52%	0.00%	NA
Tropical Japonica	504	5.00%	94.80%	0.20%	0.00%	NA
Japonica Intermediate	241	19.10%	80.90%	0.00%	0.00%	NA
VI/Aromatic	96	95.80%	4.20%	0.00%	0.00%	NA
Intermediate	90	58.90%	41.10%	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
vg0430989073	T -> C	LOC_Os04g52140-LOC_Os04g52164	intergenic_region ; MODIFIER	silent_mutation	Average:56.701; most accessible tissue: Zhenshan97 flower, score: 71.382	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0430989073	NA	9.84E-06	mr1210	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
vg0430989073	NA	1.32E-10	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
vg0430989073	NA	1.09E-07	mr1666	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
vg0430989073	NA	4.03E-07	mr1761	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
vg0430989073	NA	1.01E-07	mr1062_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
vg0430989073	NA	1.94E-10	mr1349_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
vg0430989073	NA	2.86E-07	mr1355_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
vg0430989073	NA	7.35E-06	mr1405_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
vg0430989073	NA	9.57E-07	mr1452_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
vg0430989073	NA	3.05E-06	mr1462_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
vg0430989073	NA	2.25E-06	mr1470_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
vg0430989073	NA	5.41E-07	mr1479_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
vg0430989073	2.91E-06	1.82E-19	mr1666_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
vg0430989073	NA	2.94E-06	mr1666_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
vg0430989073	NA	4.01E-39	mr1745_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
vg0430989073	6.95E-07	5.34E-18	mr1761_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
vg0430989073	NA	3.52E-08	mr1761_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
vg0430989073	4.95E-06	2.85E-10	mr1786_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
vg0430989073	NA	1.82E-08	mr1940_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