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Detailed information for vg0401488173:

Variant ID: vg0401488173 (JBrowse)	Variation Type: SNP
Chromosome: chr04	Position: 1488173
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.00, others allele: 0.00, population size: 209. )

Flanking Sequence (100 bp) in Reference Genome:

TGAACGCATCTTCGGCTTCCTGAGTCCACACAAATTTGTCTTGTTTCTTCAGCAGAGCGAAGAAGGGTTGTCCTCGTTCTCCCATCCTAGCGACGAATCT[G/A]
CTCAATGCCGCCATGCATCCAGTTAGCTTCTGGACTTCCTTGAGTCTTGTGGACGACTTCATATTCTCGATTGCCTTGATCTTCTTGGGATTTACTTCGA

Reverse complement sequence

TCGAAGTAAATCCCAAGAAGATCAAGGCAATCGAGAATATGAAGTCGTCCACAAGACTCAAGGAAGTCCAGAAGCTAACTGGATGCATGGCGGCATTGAG[C/T]
AGATTCGTCGCTAGGATGGGAGAACGAGGACAACCCTTCTTCGCTCTGCTGAAGAAACAAGACAAATTTGTGTGGACTCAGGAAGCCGAAGATGCGTTCA

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	92.80%	3.10%	1.25%	2.77%	NA
All Indica	2759	99.90%	0.00%	0.04%	0.00%	NA
All Japonica	1512	81.50%	6.50%	3.57%	8.40%	NA
Aus	269	100.00%	0.00%	0.00%	0.00%	NA
Indica I	595	100.00%	0.00%	0.00%	0.00%	NA
Indica II	465	99.80%	0.00%	0.22%	0.00%	NA
Indica III	913	99.90%	0.10%	0.00%	0.00%	NA
Indica Intermediate	786	100.00%	0.00%	0.00%	0.00%	NA
Temperate Japonica	767	79.30%	9.30%	1.83%	9.65%	NA
Tropical Japonica	504	87.70%	0.20%	5.56%	6.55%	NA
Japonica Intermediate	241	75.90%	10.80%	4.98%	8.30%	NA
VI/Aromatic	96	43.80%	47.90%	4.17%	4.17%	NA
Intermediate	90	96.70%	3.30%	0.00%	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
vg0401488173	G -> DEL	LOC_Os04g03450.1	N	frameshift_variant	Average:26.38; most accessible tissue: Minghui63 young leaf, score: 43.347	N	N	N	N
vg0401488173	G -> A	LOC_Os04g03450.1	synonymous_variant ; p.Ser965Ser; LOW	synonymous_codon	Average:26.38; most accessible tissue: Minghui63 young leaf, score: 43.347	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0401488173	NA	2.71E-22	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
vg0401488173	NA	3.81E-08	Awn_length	Jap_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
vg0401488173	NA	3.71E-06	mr1071	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
vg0401488173	NA	3.04E-06	mr1080	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
vg0401488173	NA	6.18E-06	mr1100	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
vg0401488173	NA	7.28E-06	mr1140	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
vg0401488173	6.00E-07	1.97E-08	mr1201	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
vg0401488173	NA	7.60E-06	mr1219	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
vg0401488173	NA	7.65E-06	mr1274	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
vg0401488173	NA	2.39E-06	mr1613	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
vg0401488173	NA	5.00E-06	mr1619	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
vg0401488173	NA	4.66E-08	mr1057_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
vg0401488173	2.19E-06	8.43E-08	mr1274_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
vg0401488173	NA	3.70E-07	mr1465_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