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Detailed information for vg0518975375:

Variant ID: vg0518975375 (JBrowse)	Variation Type: SNP
Chromosome: chr05	Position: 18975375
Reference Allele: T	Alternative Allele: G
Primary Allele: G	Secondary Allele: T

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.86, T: 0.13, others allele: 0.00, population size: 250. )

Flanking Sequence (100 bp) in Reference Genome:

GCCATACATTAGTATAGACAGCACTGCTTTAAATGGCAGATGGAATGGCCACTTAGCATCTGCTACAGCTGTAGATGGGCATAATTGGATGTATCCTCTT[T/G]
CTATTGGGTTTATAGATTTAGAGACTGAGGATAACTGGGAGTGGTTCATGAGTCAGCTTCATGCTGCCATAGGAGATGTTAACCCTCTAGCTGTATGCAC

Reverse complement sequence

GTGCATACAGCTAGAGGGTTAACATCTCCTATGGCAGCATGAAGCTGACTCATGAACCACTCCCAGTTATCCTCAGTCTCTAAATCTATAAACCCAATAG[A/C]
AAGAGGATACATCCAATTATGCCCATCTACAGCTGTAGCAGATGCTAAGTGGCCATTCCATCTGCCATTTAAAGCAGTGCTGTCTATACTAATGTATGGC

Allele Frequencies:

Populations	Population Size	Frequency of G(primary allele)	Frequency of T(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	53.90%	30.20%	0.55%	15.34%	NA
All Indica	2759	71.90%	1.20%	0.87%	26.10%	NA
All Japonica	1512	15.50%	84.20%	0.00%	0.26%	NA
Aus	269	99.30%	0.70%	0.00%	0.00%	NA
Indica I	595	39.50%	0.50%	1.51%	58.49%	NA
Indica II	465	89.00%	1.70%	0.22%	9.03%	NA
Indica III	913	73.80%	1.10%	0.55%	24.53%	NA
Indica Intermediate	786	84.00%	1.40%	1.15%	13.49%	NA
Temperate Japonica	767	5.00%	95.00%	0.00%	0.00%	NA
Tropical Japonica	504	32.50%	66.70%	0.00%	0.79%	NA
Japonica Intermediate	241	13.70%	86.30%	0.00%	0.00%	NA
VI/Aromatic	96	7.30%	92.70%	0.00%	0.00%	NA
Intermediate	90	63.30%	33.30%	2.22%	1.11%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0518975375	T -> DEL	LOC_Os05g32480.1	N	frameshift_variant	Average:36.042; most accessible tissue: Minghui63 young leaf, score: 68.745	N	N	N	N
vg0518975375	T -> G	LOC_Os05g32480.1	missense_variant ; p.Ser495Ala; MODERATE	nonsynonymous_codon ; S495A	Average:36.042; most accessible tissue: Minghui63 young leaf, score: 68.745	benign	-0.495	TOLERATED	1.00

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0518975375	NA	8.29E-10	mr1277	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
vg0518975375	NA	8.41E-06	mr1277	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
vg0518975375	2.27E-09	NA	mr1301	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
vg0518975375	1.36E-07	4.12E-16	mr1301	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
vg0518975375	6.07E-13	8.52E-14	mr1410	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
vg0518975375	2.64E-07	6.73E-14	mr1410	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
vg0518975375	NA	6.37E-33	mr1733	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
vg0518975375	NA	2.13E-07	mr1746	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
vg0518975375	3.31E-11	NA	mr1301_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
vg0518975375	6.84E-09	2.32E-17	mr1301_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
vg0518975375	1.69E-16	NA	mr1410_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
vg0518975375	2.68E-09	1.23E-14	mr1410_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
vg0518975375	NA	3.04E-06	mr1558_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
vg0518975375	NA	1.57E-07	mr1676_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