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Detailed information for vg0401767979:

Variant ID: vg0401767979 (JBrowse)	Variation Type: SNP
Chromosome: chr04	Position: 1767979
Reference Allele: A	Alternative Allele: G
Primary Allele: A	Secondary Allele: G

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 1.00, others allele: 0.00, population size: 90. )

Flanking Sequence (100 bp) in Reference Genome:

GCCGCCACCAGTGCACGAGGTTCGCCAGCATCGAGCCACTGAAGCCCTTGACCACGACGTCGAGCTTCAACTCCTGCATCACGCGCCGTAGGTCGCGCAC[A/G]
TGGCGCTCGTCGATGTCGTCGCCGAAGCAGAAGCGCACGGCCAGCGGGAACAAGGCGTCGTGGACGACGTCGCGGACGCCCACCTCGCCGCCGTCGGCAC

Reverse complement sequence

GTGCCGACGGCGGCGAGGTGGGCGTCCGCGACGTCGTCCACGACGCCTTGTTCCCGCTGGCCGTGCGCTTCTGCTTCGGCGACGACATCGACGAGCGCCA[T/C]
GTGCGCGACCTACGGCGCGTGATGCAGGAGTTGAAGCTCGACGTCGTGGTCAAGGGCTTCAGTGGCTCGATGCTGGCGAACCTCGTGCACTGGTGGCGGC

Allele Frequencies:

Populations	Population Size	Frequency of A(primary allele)	Frequency of G(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	53.10%	16.40%	2.03%	28.48%	NA
All Indica	2759	31.10%	19.20%	3.04%	46.65%	NA
All Japonica	1512	97.20%	1.70%	0.00%	1.19%	NA
Aus	269	33.50%	58.40%	2.23%	5.95%	NA
Indica I	595	15.50%	2.90%	2.18%	79.50%	NA
Indica II	465	40.20%	24.90%	3.01%	31.83%	NA
Indica III	913	38.30%	28.50%	3.40%	29.79%	NA
Indica Intermediate	786	29.10%	17.40%	3.31%	50.13%	NA
Temperate Japonica	767	99.90%	0.10%	0.00%	0.00%	NA
Tropical Japonica	504	93.10%	4.00%	0.00%	2.98%	NA
Japonica Intermediate	241	97.10%	1.70%	0.00%	1.24%	NA
VI/Aromatic	96	52.10%	44.80%	2.08%	1.04%	NA
Intermediate	90	48.90%	20.00%	4.44%	26.67%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0401767979	A -> DEL	LOC_Os04g03870.1	N	frameshift_variant	Average:65.123; most accessible tissue: Zhenshan97 young leaf, score: 85.184	N	N	N	N
vg0401767979	A -> G	LOC_Os04g03870.1	synonymous_variant ; p.His157His; LOW	synonymous_codon	Average:65.123; most accessible tissue: Zhenshan97 young leaf, score: 85.184	N	N	N	N
vg0401767979	A -> G	LOC_Os04g03870.1	synonymous_variant ; p.His157His; LOW	nonsynonymous_codon ; H157D	Average:65.123; most accessible tissue: Zhenshan97 young leaf, score: 85.184	unknown	unknown	TOLERATED	0.51

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0401767979	5.35E-07	NA	mr1472_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
vg0401767979	4.54E-06	NA	mr1472_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
vg0401767979	4.92E-06	4.92E-06	mr1666_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