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Detailed information for vg0141375211:

Variant ID: vg0141375211 (JBrowse)	Variation Type: SNP
Chromosome: chr01	Position: 41375211
Reference Allele: T	Alternative Allele: A
Primary Allele: T	Secondary Allele: A

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.98, A: 0.02, others allele: 0.00, population size: 272. )

Flanking Sequence (100 bp) in Reference Genome:

AGGGGTGCCTTCTCACGTTGTACATCAATCAACCATCTTGTAGCAGCTACACGGTGAAGAGATGGCAGGGCAGGGTGTTGCCTGCGCGCTAGCCGTCGCA[T/A]
TGTTCATCGGGTCCCTCGTGTCCATCCCTACAGGTAATATATATGCAGATATATTTTGATCCACCAGTTTACACGCCAGGAATTAAACCATGCAGAACAC

Reverse complement sequence

GTGTTCTGCATGGTTTAATTCCTGGCGTGTAAACTGGTGGATCAAAATATATCTGCATATATATTACCTGTAGGGATGGACACGAGGGACCCGATGAACA[A/T]
TGCGACGGCTAGCGCGCAGGCAACACCCTGCCCTGCCATCTCTTCACCGTGTAGCTGCTACAAGATGGTTGATTGATGTACAACGTGAGAAGGCACCCCT

Allele Frequencies:

Populations	Population Size	Frequency of T(primary allele)	Frequency of A(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	66.70%	32.70%	0.15%	0.42%	NA
All Indica	2759	45.50%	53.60%	0.25%	0.58%	NA
All Japonica	1512	98.40%	1.50%	0.00%	0.13%	NA
Aus	269	93.30%	6.70%	0.00%	0.00%	NA
Indica I	595	83.00%	16.60%	0.17%	0.17%	NA
Indica II	465	12.50%	86.00%	0.22%	1.29%	NA
Indica III	913	35.50%	64.50%	0.00%	0.00%	NA
Indica Intermediate	786	48.30%	49.90%	0.64%	1.15%	NA
Temperate Japonica	767	99.60%	0.40%	0.00%	0.00%	NA
Tropical Japonica	504	96.20%	3.40%	0.00%	0.40%	NA
Japonica Intermediate	241	99.20%	0.80%	0.00%	0.00%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	68.90%	28.90%	0.00%	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
vg0141375211	T -> A	LOC_Os01g71410.1	missense_variant ; p.Leu14Met; MODERATE	nonsynonymous_codon ; L14M	Average:63.305; most accessible tissue: Callus, score: 88.048	unknown	unknown	DELETERIOUS	0.04
vg0141375211	T -> DEL	LOC_Os01g71410.1	N	frameshift_variant	Average:63.305; most accessible tissue: Callus, score: 88.048	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0141375211	NA	3.44E-16	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
vg0141375211	NA	1.75E-16	Grain_length	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
vg0141375211	NA	5.59E-08	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
vg0141375211	NA	3.63E-14	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
vg0141375211	NA	2.30E-06	mr1399	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
vg0141375211	NA	5.25E-07	mr1458	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
vg0141375211	NA	1.22E-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
vg0141375211	NA	2.20E-10	mr1319_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
vg0141375211	NA	3.03E-09	mr1322_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
vg0141375211	NA	7.10E-06	mr1323_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
vg0141375211	NA	4.96E-15	mr1330_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
vg0141375211	NA	5.22E-06	mr1438_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
vg0141375211	NA	1.44E-07	mr1458_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
vg0141375211	NA	1.31E-07	mr1527_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