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Detailed information for vg0142134296:

Variant ID: vg0142134296 (JBrowse)	Variation Type: SNP
Chromosome: chr01	Position: 42134296
Reference Allele: C	Alternative Allele: A,T
Primary Allele: C	Secondary Allele: A

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.85, A: 0.13, T: 0.03, others allele: 0.00, population size: 78. )

Flanking Sequence (100 bp) in Reference Genome:

CGTGACTGTAAGTACTGAACTACTCACATCCATTGCGTTTTGACAAATTGACCCTTTTCAAAAACTTATTTCGAAACTAACCTCTGCCAAAAACTTCAAC[C/A,T]
AAAAATAAGCCGTCGGCTCAGCGCCAAGGGTCTTGGCGCTGATGTTGTGCATGAAAGCGCCAACATGCTTGGCGCTGACATTGTGCCACCGTGGCGGCCG

Reverse complement sequence

CGGCCGCCACGGTGGCACAATGTCAGCGCCAAGCATGTTGGCGCTTTCATGCACAACATCAGCGCCAAGACCCTTGGCGCTGAGCCGACGGCTTATTTTT[G/T,A]
GTTGAAGTTTTTGGCAGAGGTTAGTTTCGAAATAAGTTTTTGAAAAGGGTCAATTTGTCAAAACGCAATGGATGTGAGTAGTTCAGTACTTACAGTCACG

Allele Frequencies:

Populations	Population Size	Frequency of C(primary allele)	Frequency of A(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	74.70%	22.60%	0.68%	2.01%	NA
All Indica	2759	79.10%	20.00%	0.36%	0.62%	NA
All Japonica	1512	61.20%	32.30%	1.39%	5.03%	NA
Aus	269	99.60%	0.40%	0.00%	0.00%	NA
Indica I	595	75.00%	23.40%	0.17%	1.51%	NA
Indica II	465	86.50%	13.10%	0.43%	0.00%	NA
Indica III	913	83.50%	16.30%	0.11%	0.11%	NA
Indica Intermediate	786	72.60%	25.70%	0.76%	0.89%	NA
Temperate Japonica	767	89.30%	10.30%	0.39%	0.00%	NA
Tropical Japonica	504	15.10%	68.50%	2.38%	14.09%	NA
Japonica Intermediate	241	68.50%	27.00%	2.49%	2.07%	NA
VI/Aromatic	96	96.90%	3.10%	0.00%	0.00%	NA
Intermediate	90	71.10%	25.60%	1.11%	2.22%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0142134296	C -> T	LOC_Os01g72620.1	missense_variant ; p.Gly410Ser; MODERATE	N	Average:79.733; most accessible tissue: Callus, score: 90.828	N	N	N	N
vg0142134296	C -> T	LOC_Os01g72610.1	upstream_gene_variant ; 3949.0bp to feature; MODIFIER	N	Average:79.733; most accessible tissue: Callus, score: 90.828	N	N	N	N
vg0142134296	C -> T	LOC_Os01g72630.1	upstream_gene_variant ; 4353.0bp to feature; MODIFIER	N	Average:79.733; most accessible tissue: Callus, score: 90.828	N	N	N	N
vg0142134296	C -> A	LOC_Os01g72620.1	missense_variant ; p.Gly410Cys; MODERATE	nonsynonymous_codon ; G410C	Average:79.733; most accessible tissue: Callus, score: 90.828	unknown	unknown	DELETERIOUS	0.00
vg0142134296	C -> DEL	LOC_Os01g72620.1	N	frameshift_variant	Average:79.733; most accessible tissue: Callus, score: 90.828	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0142134296	NA	9.49E-11	Grain_weight	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
vg0142134296	NA	3.55E-11	mr1553	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
vg0142134296	NA	1.53E-09	mr1039_2	Jap_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
vg0142134296	NA	1.92E-13	mr1553_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
vg0142134296	NA	1.73E-08	mr1632_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