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Detailed information for vg0404710590:

Variant ID: vg0404710590 (JBrowse)	Variation Type: SNP
Chromosome: chr04	Position: 4710590
Reference Allele: T	Alternative Allele: C
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.53, C: 0.47, others allele: 0.00, population size: 88. )

Flanking Sequence (100 bp) in Reference Genome:

GGAGACGGAGGAAGAGCGGCAGGCAGCACTGATTGCCTCAAGCGTCCTAGATGAAGCGCTGGGCGACATCCGCTTACAGTACGAGGTCCATGCCGAGGAC[T/C]
TGACGAAGAGGGTTAAGGACGCCCGTGGTGTCCTCGATGCGGCTGCCGCCCAAGAGCAGCGCGAGTCCACCTTGGCTGCCCACGAGAGAATGGCGGCGGA

Reverse complement sequence

TCCGCCGCCATTCTCTCGTGGGCAGCCAAGGTGGACTCGCGCTGCTCTTGGGCGGCAGCCGCATCGAGGACACCACGGGCGTCCTTAACCCTCTTCGTCA[A/G]
GTCCTCGGCATGGACCTCGTACTGTAAGCGGATGTCGCCCAGCGCTTCATCTAGGACGCTTGAGGCAATCAGTGCTGCCTGCCGCTCTTCCTCCGTCTCC

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	63.50%	36.30%	0.17%	0.04%	NA
All Indica	2759	91.80%	7.90%	0.25%	0.07%	NA
All Japonica	1512	8.10%	91.90%	0.00%	0.00%	NA
Aus	269	94.40%	5.20%	0.37%	0.00%	NA
Indica I	595	98.70%	1.30%	0.00%	0.00%	NA
Indica II	465	91.40%	7.10%	1.08%	0.43%	NA
Indica III	913	86.30%	13.70%	0.00%	0.00%	NA
Indica Intermediate	786	93.30%	6.50%	0.25%	0.00%	NA
Temperate Japonica	767	0.70%	99.30%	0.00%	0.00%	NA
Tropical Japonica	504	19.80%	80.20%	0.00%	0.00%	NA
Japonica Intermediate	241	7.50%	92.50%	0.00%	0.00%	NA
VI/Aromatic	96	40.60%	59.40%	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
vg0404710590	T -> C	LOC_Os04g08670.1	synonymous_variant ; p.Leu489Leu; LOW	synonymous_codon	Average:70.902; most accessible tissue: Zhenshan97 flag leaf, score: 86.452	N	N	N	N
vg0404710590	T -> DEL	LOC_Os04g08670.1	N	frameshift_variant	Average:70.902; most accessible tissue: Zhenshan97 flag leaf, score: 86.452	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0404710590	NA	4.84E-08	mr1514	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
vg0404710590	NA	6.35E-08	mr1020_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
vg0404710590	6.70E-06	NA	mr1060_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
vg0404710590	6.82E-06	6.82E-06	mr1172_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
vg0404710590	2.84E-06	NA	mr1439_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
vg0404710590	2.56E-06	2.56E-06	mr1439_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
vg0404710590	NA	1.40E-08	mr1576_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
vg0404710590	NA	6.10E-10	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