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Detailed information for vg0507092737:

Variant ID: vg0507092737 (JBrowse)	Variation Type: SNP
Chromosome: chr05	Position: 7092737
Reference Allele: A	Alternative Allele: G
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.00, others allele: 0.00, population size: 218. )

Flanking Sequence (100 bp) in Reference Genome:

CTCCTTCGAAGCAAAAGAAGAAGGAATGAAGAGGTATCTGGAGGCTGTTCGGTTCATGGAAAAATACTTCACTGGCATAACGGTCGAACACTTACCTAGA[A/G]
GCCAGAACGAGGAAGCAGACGCCCTGGCGAAATCCGCTGCTTGTGGTGGCCCACATTCGCCTGGCATCTTTTTCGAAGTCCTACATGCTCCAAGTGTGTC

Reverse complement sequence

GACACACTTGGAGCATGTAGGACTTCGAAAAAGATGCCAGGCGAATGTGGGCCACCACAAGCAGCGGATTTCGCCAGGGCGTCTGCTTCCTCGTTCTGGC[T/C]
TCTAGGTAAGTGTTCGACCGTTATGCCAGTGAAGTATTTTTCCATGAACCGAACAGCCTCCAGATACCTCTTCATTCCTTCTTCTTTTGCTTCGAAGGAG

Allele Frequencies:

Populations	Population Size	Frequency of G(primary allele)	Frequency of A(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	47.20%	19.20%	13.54%	20.04%	NA
All Indica	2759	67.30%	1.10%	17.65%	13.99%	NA
All Japonica	1512	6.70%	56.70%	5.95%	30.62%	NA
Aus	269	86.20%	0.40%	9.67%	3.72%	NA
Indica I	595	84.50%	1.00%	6.72%	7.73%	NA
Indica II	465	41.70%	2.40%	31.40%	24.52%	NA
Indica III	913	64.20%	0.40%	20.48%	14.90%	NA
Indica Intermediate	786	72.90%	1.10%	14.50%	11.45%	NA
Temperate Japonica	767	0.90%	91.30%	0.78%	7.04%	NA
Tropical Japonica	504	11.10%	9.70%	14.48%	64.68%	NA
Japonica Intermediate	241	15.80%	45.20%	4.56%	34.44%	NA
VI/Aromatic	96	8.30%	1.00%	20.83%	69.79%	NA
Intermediate	90	38.90%	18.90%	18.89%	23.33%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0507092737	A -> DEL	LOC_Os05g12340.1	N	frameshift_variant	Average:38.531; most accessible tissue: Minghui63 flag leaf, score: 68.675	N	N	N	N
vg0507092737	A -> G	LOC_Os05g12340.1	missense_variant ; p.Ser677Gly; MODERATE	nonsynonymous_codon ; S677G	Average:38.531; most accessible tissue: Minghui63 flag leaf, score: 68.675	benign	-0.806	TOLERATED	1.00

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0507092737	NA	7.82E-39	Grain_thickness	All	Not	Breeding signatures of rice improvement revealed by a genomic variation map from a large germplasm collection, Proc Natl Acad Sci USA, 112(39): E5411-E5419, PMID:26358652
vg0507092737	NA	1.41E-06	mr1401	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
vg0507092737	NA	1.24E-08	mr1549	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
vg0507092737	NA	3.16E-08	mr1552	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
vg0507092737	2.33E-08	5.95E-11	mr1593	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
vg0507092737	2.32E-10	2.26E-26	mr1593	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
vg0507092737	NA	2.17E-07	mr1723	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
vg0507092737	5.42E-07	NA	mr1829	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
vg0507092737	NA	1.04E-07	mr1916	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
vg0507092737	NA	4.34E-30	mr1980	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
vg0507092737	NA	5.52E-06	mr1039_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
vg0507092737	NA	5.38E-10	mr1093_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
vg0507092737	5.26E-06	NA	mr1593_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
vg0507092737	5.92E-16	1.55E-39	mr1593_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