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Detailed information for vg0431867782:

Variant ID: vg0431867782 (JBrowse)	Variation Type: SNP
Chromosome: chr04	Position: 31867782
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.99, others allele: 0.00, population size: 232. )

Flanking Sequence (100 bp) in Reference Genome:

GCGGTTACAACAGGCACGCCCCTCTATTTATGAGAGATCCTAGGATAAAATCCGACTCATACTCTAGTCCTACACTTAGTACAACTCCAAGTCCTAAACT[G/A]
TAACCGACTACGTACACATATTCGACACAAACTCTAACAAACTCCACCTTGGCGAATATGCCACGCCAACCTGAATTCATTACTTGCTCGAACCTCCATG

Reverse complement sequence

CATGGAGGTTCGAGCAAGTAATGAATTCAGGTTGGCGTGGCATATTCGCCAAGGTGGAGTTTGTTAGAGTTTGTGTCGAATATGTGTACGTAGTCGGTTA[C/T]
AGTTTAGGACTTGGAGTTGTACTAAGTGTAGGACTAGAGTATGAGTCGGATTTTATCCTAGGATCTCTCATAAATAGAGGGGCGTGCCTGTTGTAACCGC

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	68.50%	21.30%	6.12%	4.06%	NA
All Indica	2759	74.20%	10.10%	10.08%	5.69%	NA
All Japonica	1512	62.70%	34.70%	0.46%	2.18%	NA
Aus	269	43.50%	56.10%	0.37%	0.00%	NA
Indica I	595	65.40%	3.90%	13.78%	16.97%	NA
Indica II	465	81.10%	8.20%	8.82%	1.94%	NA
Indica III	913	77.40%	14.20%	6.79%	1.53%	NA
Indica Intermediate	786	72.90%	11.10%	11.83%	4.20%	NA
Temperate Japonica	767	89.20%	10.30%	0.13%	0.39%	NA
Tropical Japonica	504	32.70%	60.70%	1.19%	5.36%	NA
Japonica Intermediate	241	41.10%	57.70%	0.00%	1.24%	NA
VI/Aromatic	96	60.40%	39.60%	0.00%	0.00%	NA
Intermediate	90	76.70%	17.80%	3.33%	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
vg0431867782	G -> DEL	N	N	silent_mutation	Average:49.411; most accessible tissue: Minghui63 panicle, score: 84.552	N	N	N	N
vg0431867782	G -> A	LOC_Os04g53496-LOC_Os04g53510	intergenic_region ; MODIFIER	silent_mutation	Average:49.411; most accessible tissue: Minghui63 panicle, score: 84.552	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0431867782	NA	6.52E-17	Plant_height	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
vg0431867782	NA	2.40E-12	Spikelet_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
vg0431867782	NA	9.27E-06	mr1318	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
vg0431867782	NA	4.52E-06	mr1531	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
vg0431867782	NA	4.56E-07	mr1617	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
vg0431867782	NA	5.85E-07	mr1043_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
vg0431867782	4.51E-06	NA	mr1133_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
vg0431867782	NA	5.56E-07	mr1229_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
vg0431867782	NA	1.05E-06	mr1269_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
vg0431867782	NA	2.17E-06	mr1456_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
vg0431867782	NA	3.93E-06	mr1617_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
vg0431867782	NA	9.61E-06	mr1677_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
vg0431867782	NA	8.86E-07	mr1729_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
vg0431867782	NA	8.02E-08	mr1880_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