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Detailed information for vg0307395283:

Variant ID: vg0307395283 (JBrowse)	Variation Type: SNP
Chromosome: chr03	Position: 7395283
Reference Allele: C	Alternative Allele: G
Primary Allele: C	Secondary Allele: G

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.95, C: 0.05, others allele: 0.00, population size: 81. )

Flanking Sequence (100 bp) in Reference Genome:

CAAGTTAAATGGACGATCCAAGGGATTAAAAGAGAGGGAATTACAATGAGACAAGATAGTTCACCCTCTAGAGAGGGAATGTGTGAATCTATTTCAAGTT[C/G]
TGCTAGGACCAAAATTCATTGAAAAATGAGATCCCCATACAAATAGATTCAAGTTCTCCACAAAAGTGACTAGTGTCCATCCATGAGTTGAAAGACCATT

Reverse complement sequence

AATGGTCTTTCAACTCATGGATGGACACTAGTCACTTTTGTGGAGAACTTGAATCTATTTGTATGGGGATCTCATTTTTCAATGAATTTTGGTCCTAGCA[G/C]
AACTTGAAATAGATTCACACATTCCCTCTCTAGAGGGTGAACTATCTTGTCTCATTGTAATTCCCTCTCTTTTAATCCCTTGGATCGTCCATTTAACTTG

Allele Frequencies:

Populations	Population Size	Frequency of C(primary allele)	Frequency of G(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	29.30%	2.90%	8.74%	59.06%	NA
All Indica	2759	2.20%	0.20%	11.05%	86.52%	NA
All Japonica	1512	84.90%	8.20%	0.07%	6.81%	NA
Aus	269	1.10%	0.00%	38.66%	60.22%	NA
Indica I	595	3.20%	0.00%	4.71%	92.10%	NA
Indica II	465	2.40%	0.40%	3.44%	93.76%	NA
Indica III	913	0.80%	0.00%	19.82%	79.41%	NA
Indica Intermediate	786	3.20%	0.40%	10.18%	86.26%	NA
Temperate Japonica	767	81.40%	15.60%	0.00%	3.00%	NA
Tropical Japonica	504	85.30%	0.20%	0.20%	14.29%	NA
Japonica Intermediate	241	95.40%	1.20%	0.00%	3.32%	NA
VI/Aromatic	96	3.10%	2.10%	2.08%	92.71%	NA
Intermediate	90	36.70%	6.70%	1.11%	55.56%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0307395283	C -> DEL	N	N	silent_mutation	Average:8.436; most accessible tissue: Callus, score: 38.937	N	N	N	N
vg0307395283	C -> G	LOC_Os03g13680.1	downstream_gene_variant ; 2502.0bp to feature; MODIFIER	silent_mutation	Average:8.436; most accessible tissue: Callus, score: 38.937	N	N	N	N
vg0307395283	C -> G	LOC_Os03g13670.1	intron_variant ; MODIFIER	silent_mutation	Average:8.436; most accessible tissue: Callus, score: 38.937	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0307395283	NA	4.19E-07	mr1171	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
vg0307395283	NA	3.01E-07	mr1358	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
vg0307395283	4.80E-06	4.80E-06	mr1655	Jap_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
vg0307395283	NA	2.14E-09	mr1712	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
vg0307395283	NA	1.95E-07	mr1715	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
vg0307395283	NA	8.97E-08	mr1946	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
vg0307395283	NA	8.03E-06	mr1977	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