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Detailed information for vg0628049712:

Variant ID: vg0628049712 (JBrowse)	Variation Type: SNP
Chromosome: chr06	Position: 28049712
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.99, others allele: 0.00, population size: 107. )

Flanking Sequence (100 bp) in Reference Genome:

CGCGAACCGGTCCTTAATCGCCATGGGCACGACTAGCAAAATCATGCACCCACAGCTCACCATGTAGTGTATTTTAATTAACCAACACCATAGCGGTGGC[G/A]
CTAATCCAACAATACCATTAGAACCAACAGTCTAAACATTAATAGGATTCTCCCTATTGTGCACTAGTTGAACTAAGCATGGCTAAGCAATCCCTAGTCC

Reverse complement sequence

GGACTAGGGATTGCTTAGCCATGCTTAGTTCAACTAGTGCACAATAGGGAGAATCCTATTAATGTTTAGACTGTTGGTTCTAATGGTATTGTTGGATTAG[C/T]
GCCACCGCTATGGTGTTGGTTAATTAAAATACACTACATGGTGAGCTGTGGGTGCATGATTTTGCTAGTCGTGCCCATGGCGATTAAGGACCGGTTCGCG

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	27.80%	6.20%	9.18%	56.77%	NA
All Indica	2759	1.80%	0.30%	14.35%	83.51%	NA
All Japonica	1512	80.90%	12.80%	1.46%	4.89%	NA
Aus	269	0.40%	1.50%	4.83%	93.31%	NA
Indica I	595	1.30%	0.00%	7.73%	90.92%	NA
Indica II	465	2.40%	0.00%	6.02%	91.61%	NA
Indica III	913	0.90%	0.20%	24.86%	74.04%	NA
Indica Intermediate	786	2.90%	0.90%	12.09%	84.10%	NA
Temperate Japonica	767	77.10%	19.70%	0.00%	3.26%	NA
Tropical Japonica	504	82.30%	6.00%	4.17%	7.54%	NA
Japonica Intermediate	241	90.00%	5.00%	0.41%	4.56%	NA
VI/Aromatic	96	14.60%	81.20%	1.04%	3.12%	NA
Intermediate	90	30.00%	11.10%	2.22%	56.67%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0628049712	G -> A	LOC_Os06g46284.1	intron_variant ; MODIFIER	silent_mutation	Average:14.097; most accessible tissue: Callus, score: 26.174	N	N	N	N
vg0628049712	G -> A	LOC_Os06g46284.2	intron_variant ; MODIFIER	silent_mutation	Average:14.097; most accessible tissue: Callus, score: 26.174	N	N	N	N
vg0628049712	G -> DEL	N	N	silent_mutation	Average:14.097; most accessible tissue: Callus, score: 26.174	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0628049712	NA	1.19E-16	Awn_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
vg0628049712	1.31E-10	NA	mr1210	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
vg0628049712	NA	5.30E-09	mr1210	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
vg0628049712	1.19E-07	NA	mr1305	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
vg0628049712	NA	7.41E-07	mr1305	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
vg0628049712	9.04E-06	9.04E-06	mr1409	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
vg0628049712	1.98E-06	1.45E-12	mr1585	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
vg0628049712	NA	7.18E-08	mr1585	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
vg0628049712	1.13E-10	NA	mr1586	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
vg0628049712	NA	2.71E-09	mr1586	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
vg0628049712	2.10E-06	NA	mr1672	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
vg0628049712	4.99E-07	NA	mr1765	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
vg0628049712	NA	2.94E-06	mr1765	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
vg0628049712	4.69E-07	NA	mr1166_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
vg0628049712	5.96E-06	5.96E-06	mr1166_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
vg0628049712	5.83E-09	NA	mr1305_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
vg0628049712	7.33E-06	2.76E-08	mr1305_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
vg0628049712	4.55E-08	6.44E-16	mr1585_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
vg0628049712	NA	3.26E-09	mr1585_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
vg0628049712	3.58E-08	NA	mr1672_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
vg0628049712	NA	8.44E-06	mr1765_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