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Detailed information for vg0505358972:

Variant ID: vg0505358972 (JBrowse)	Variation Type: SNP
Chromosome: chr05	Position: 5358972
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.99, T: 0.00, others allele: 0.00, population size: 254. )

Flanking Sequence (100 bp) in Reference Genome:

ATTTTGTAGGTGATAACTTTTTCATTTGAAATCTTTTAGATATTCAAATCTATGATTCAAATCTCAGTTAGGTAGGCTCAAATGGAACGATATGCATTTT[C/T]
CAACAGAATTGATGCATAGGTGAGTTGGTAAAAGAGAGCACGTGTGAAGGATAGGTCTTAAGTTCGAATCCTAGCCAAGACACGATATCAAAAAAAATAA

Reverse complement sequence

TTATTTTTTTTGATATCGTGTCTTGGCTAGGATTCGAACTTAAGACCTATCCTTCACACGTGCTCTCTTTTACCAACTCACCTATGCATCAATTCTGTTG[G/A]
AAAATGCATATCGTTCCATTTGAGCCTACCTAACTGAGATTTGAATCATAGATTTGAATATCTAAAAGATTTCAAATGAAAAAGTTATCACCTACAAAAT

Allele Frequencies:

Populations	Population Size	Frequency of C(primary allele)	Frequency of T(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	65.60%	32.50%	0.17%	1.76%	NA
All Indica	2759	53.80%	46.00%	0.11%	0.07%	NA
All Japonica	1512	84.60%	9.80%	0.26%	5.36%	NA
Aus	269	77.70%	22.30%	0.00%	0.00%	NA
Indica I	595	17.10%	82.50%	0.34%	0.00%	NA
Indica II	465	86.20%	13.80%	0.00%	0.00%	NA
Indica III	913	59.80%	40.00%	0.00%	0.22%	NA
Indica Intermediate	786	55.50%	44.40%	0.13%	0.00%	NA
Temperate Japonica	767	91.90%	7.80%	0.00%	0.26%	NA
Tropical Japonica	504	71.80%	13.30%	0.60%	14.29%	NA
Japonica Intermediate	241	88.00%	8.70%	0.41%	2.90%	NA
VI/Aromatic	96	60.40%	39.60%	0.00%	0.00%	NA
Intermediate	90	75.60%	23.30%	1.11%	0.00%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0505358972	C -> T	LOC_Os05g09510-LOC_Os05g09520	intergenic_region ; MODIFIER	silent_mutation	Average:26.111; most accessible tissue: Callus, score: 41.682	N	N	N	N
vg0505358972	C -> DEL	N	N	silent_mutation	Average:26.111; most accessible tissue: Callus, score: 41.682	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0505358972	4.40E-06	NA	Grain_length	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
vg0505358972	2.86E-08	1.88E-28	Grain_length	Ind_All	YES	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
vg0505358972	6.50E-09	2.11E-16	Grain_thickness	Ind_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
vg0505358972	1.23E-09	NA	Grain_width	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
vg0505358972	1.56E-24	5.25E-49	Grain_width	Ind_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
vg0505358972	NA	4.20E-08	mr1183	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
vg0505358972	NA	9.94E-06	mr1240	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
vg0505358972	NA	5.99E-08	mr1503	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
vg0505358972	NA	1.42E-07	mr1183_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
vg0505358972	NA	3.61E-06	mr1319_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
vg0505358972	NA	4.22E-08	mr1330_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
vg0505358972	NA	4.56E-06	mr1838_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