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Detailed information for vg0113034093:

Variant ID: vg0113034093 (JBrowse)	Variation Type: SNP
Chromosome: chr01	Position: 13034093
Reference Allele: A	Alternative Allele: G
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.99, A: 0.01, others allele: 0.00, population size: 108. )

Flanking Sequence (100 bp) in Reference Genome:

GCCGGAGAACCAAACTGGGAGGAATTTACCACAGCCTTCCGTGACAACTTCGTGCCTGCTGCGGTGATGCGGATGAAGAAGAATGAGTTCAGGAGACTAC[A/G]
GCAAGGGAATACCACAGTACAAGAGTACCTGAACCGTTTCACTCAGCTGGCGCGCTACGCGACTAGAGATCTTGCCGACGAGGAGGAAAAGATCGACAAA

Reverse complement sequence

TTTGTCGATCTTTTCCTCCTCGTCGGCAAGATCTCTAGTCGCGTAGCGCGCCAGCTGAGTGAAACGGTTCAGGTACTCTTGTACTGTGGTATTCCCTTGC[T/C]
GTAGTCTCCTGAACTCATTCTTCTTCATCCGCATCACCGCAGCAGGCACGAAGTTGTCACGGAAGGCTGTGGTAAATTCCTCCCAGTTTGGTTCTCCGGC

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	44.90%	44.20%	7.43%	3.39%	NA
All Indica	2759	66.20%	27.10%	6.27%	0.47%	NA
All Japonica	1512	11.20%	77.70%	1.39%	9.66%	NA
Aus	269	27.10%	28.60%	44.24%	0.00%	NA
Indica I	595	35.00%	50.60%	13.28%	1.18%	NA
Indica II	465	60.40%	33.30%	5.38%	0.86%	NA
Indica III	913	93.50%	4.70%	1.75%	0.00%	NA
Indica Intermediate	786	61.50%	31.60%	6.74%	0.25%	NA
Temperate Japonica	767	18.00%	80.70%	0.39%	0.91%	NA
Tropical Japonica	504	5.20%	64.90%	3.17%	26.79%	NA
Japonica Intermediate	241	2.50%	95.00%	0.83%	1.66%	NA
VI/Aromatic	96	30.20%	32.30%	37.50%	0.00%	NA
Intermediate	90	28.90%	67.80%	2.22%	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
vg0113034093	A -> G	LOC_Os01g23200.1	missense_variant ; p.Gln124Arg; MODERATE	nonsynonymous_codon ; Q124W	Average:7.868; most accessible tissue: Minghui63 panicle, score: 16.27	probably damaging	2.97	DELETERIOUS	0.00
vg0113034093	A -> G	LOC_Os01g23200.1	missense_variant ; p.Gln124Arg; MODERATE	nonsynonymous_codon ; Q124R	Average:7.868; most accessible tissue: Minghui63 panicle, score: 16.27	benign	-0.436	TOLERATED	0.64
vg0113034093	A -> DEL	LOC_Os01g23200.1	N	frameshift_variant	Average:7.868; most accessible tissue: Minghui63 panicle, score: 16.27	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0113034093	NA	3.67E-11	Plant_height	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
vg0113034093	NA	2.01E-06	mr1164	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
vg0113034093	NA	1.04E-09	mr1648	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
vg0113034093	NA	4.19E-09	mr1648	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
vg0113034093	NA	8.76E-22	mr1010_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
vg0113034093	NA	3.04E-09	mr1030_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
vg0113034093	NA	2.84E-06	mr1030_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
vg0113034093	NA	2.92E-13	mr1035_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
vg0113034093	1.56E-07	2.36E-11	mr1164_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
vg0113034093	NA	4.05E-06	mr1380_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
vg0113034093	NA	2.02E-06	mr1561_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
vg0113034093	NA	2.19E-09	mr1576_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
vg0113034093	NA	4.23E-09	mr1709_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
vg0113034093	NA	4.20E-06	mr1875_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