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Detailed information for vg0507350915:

Variant ID: vg0507350915 (JBrowse)	Variation Type: SNP
Chromosome: chr05	Position: 7350915
Reference Allele: G	Alternative Allele: A
Primary Allele: A	Secondary Allele: G

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.93, A: 0.06, others allele: 0.00, population size: 191. )

Flanking Sequence (100 bp) in Reference Genome:

CCATCGGCGGGGTGTCTCAGCATCCCGCCCTTTTGACGTTCTTCAGCGTGCCAACGTATCATTCTAGCATTCCCCTTGTTCTTGAACAAACGCCTTAGCC[G/A]
TGGTATTATAGGAAAATACCACATCACCTTAGCAGGAATTCTCTTCTTCTTTAGCTGCCCGTCAACTTCACCTGGATCATCTCGTCTAATCTTGTATCGT

Reverse complement sequence

ACGATACAAGATTAGACGAGATGATCCAGGTGAAGTTGACGGGCAGCTAAAGAAGAAGAGAATTCCTGCTAAGGTGATGTGGTATTTTCCTATAATACCA[C/T]
GGCTAAGGCGTTTGTTCAAGAACAAGGGGAATGCTAGAATGATACGTTGGCACGCTGAAGAACGTCAAAAGGGCGGGATGCTGAGACACCCCGCCGATGG

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	30.60%	24.90%	12.38%	32.04%	NA
All Indica	2759	21.80%	8.80%	17.00%	52.41%	NA
All Japonica	1512	50.30%	48.60%	0.26%	0.79%	NA
Aus	269	15.20%	34.20%	36.80%	13.75%	NA
Indica I	595	1.50%	8.10%	12.44%	77.98%	NA
Indica II	465	47.50%	4.90%	6.45%	41.08%	NA
Indica III	913	26.00%	8.90%	23.77%	41.40%	NA
Indica Intermediate	786	17.00%	11.60%	18.83%	52.54%	NA
Temperate Japonica	767	18.80%	79.90%	0.00%	1.30%	NA
Tropical Japonica	504	89.10%	9.90%	0.60%	0.40%	NA
Japonica Intermediate	241	69.70%	29.90%	0.41%	0.00%	NA
VI/Aromatic	96	10.40%	88.50%	1.04%	0.00%	NA
Intermediate	90	38.90%	26.70%	13.33%	21.11%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0507350915	G -> DEL	LOC_Os05g12804.1	N	frameshift_variant	Average:21.149; most accessible tissue: Zhenshan97 panicle, score: 36.038	N	N	N	N
vg0507350915	G -> A	LOC_Os05g12804.1	missense_variant ; p.Arg205Trp; MODERATE	nonsynonymous_codon ; R205W	Average:21.149; most accessible tissue: Zhenshan97 panicle, score: 36.038	benign	0.991	TOLERATED	0.06

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0507350915	NA	3.58E-14	Grain_thickness	Jap_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
vg0507350915	2.71E-06	2.12E-10	mr1039	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
vg0507350915	NA	1.01E-11	mr1272	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
vg0507350915	2.52E-07	4.32E-22	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
vg0507350915	NA	7.57E-14	mr1593	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
vg0507350915	1.06E-08	2.59E-22	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
vg0507350915	NA	1.37E-07	mr1668	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
vg0507350915	1.99E-07	3.39E-12	mr1039_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
vg0507350915	NA	2.74E-06	mr1077_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
vg0507350915	NA	6.54E-07	mr1188_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
vg0507350915	NA	7.35E-06	mr1428_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
vg0507350915	1.49E-09	1.05E-28	mr1593_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
vg0507350915	NA	6.20E-16	mr1593_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
vg0507350915	5.60E-09	5.87E-25	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
vg0507350915	4.23E-06	1.26E-08	mr1632_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
vg0507350915	NA	7.57E-07	mr1875_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
vg0507350915	NA	3.46E-06	mr1942_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