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Detailed information for vg0141994613:

Variant ID: vg0141994613 (JBrowse)	Variation Type: SNP
Chromosome: chr01	Position: 41994613
Reference Allele: C	Alternative Allele: A
Primary Allele: C	Secondary Allele: A

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, others allele: 0.00, population size: 112. )

Flanking Sequence (100 bp) in Reference Genome:

TACCAGACCATACCTCAATGGGAGTTTTCTTATTAAGTGGGATAGAAGGCGACCTGTTGATCAAGTAGCAGGCGGTGTTAGCAGCCTCTATCCAAAAACG[C/A]
TTGTTCATGCGAGCGTTGGACAGCATACAACGAGCCTTGGAGATGATGGTTCTGTTCATGCGCTCAGCCACACCATTCTGCTGTGGAGTGTACGGGATGG

Reverse complement sequence

CCATCCCGTACACTCCACAGCAGAATGGTGTGGCTGAGCGCATGAACAGAACCATCATCTCCAAGGCTCGTTGTATGCTGTCCAACGCTCGCATGAACAA[G/T]
CGTTTTTGGATAGAGGCTGCTAACACCGCCTGCTACTTGATCAACAGGTCGCCTTCTATCCCACTTAATAAGAAAACTCCCATTGAGGTATGGTCTGGTA

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	79.10%	15.70%	4.80%	0.34%	NA
All Indica	2759	66.70%	26.40%	6.85%	0.04%	NA
All Japonica	1512	96.60%	0.30%	2.25%	0.93%	NA
Aus	269	99.30%	0.40%	0.37%	0.00%	NA
Indica I	595	88.60%	0.00%	11.43%	0.00%	NA
Indica II	465	30.30%	66.50%	3.23%	0.00%	NA
Indica III	913	68.20%	25.00%	6.68%	0.11%	NA
Indica Intermediate	786	69.80%	24.40%	5.73%	0.00%	NA
Temperate Japonica	767	99.70%	0.30%	0.00%	0.00%	NA
Tropical Japonica	504	90.30%	0.20%	6.75%	2.78%	NA
Japonica Intermediate	241	99.60%	0.40%	0.00%	0.00%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	84.40%	11.10%	3.33%	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
vg0141994613	C -> A	LOC_Os01g72400.1	missense_variant ; p.Lys611Asn; MODERATE	nonsynonymous_codon ; K611N	Average:18.002; most accessible tissue: Zhenshan97 panicle, score: 28.447	benign	0.747	DELETERIOUS	0.03
vg0141994613	C -> DEL	LOC_Os01g72400.1	N	frameshift_variant	Average:18.002; most accessible tissue: Zhenshan97 panicle, score: 28.447	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0141994613	NA	2.51E-07	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
vg0141994613	NA	6.19E-12	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
vg0141994613	NA	2.50E-06	mr1122	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
vg0141994613	NA	6.85E-06	mr1383	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
vg0141994613	NA	2.36E-06	mr1629	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
vg0141994613	NA	3.83E-08	mr1666	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
vg0141994613	2.78E-06	2.78E-06	mr1666	Ind_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
vg0141994613	NA	6.39E-10	mr1720	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
vg0141994613	NA	2.95E-07	mr1720	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
vg0141994613	NA	1.07E-08	mr1935	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
vg0141994613	NA	1.71E-06	mr1974	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
vg0141994613	NA	5.03E-06	mr1974	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
vg0141994613	NA	6.96E-06	mr1974_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