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Detailed information for vg0611856752:

Variant ID: vg0611856752 (JBrowse)	Variation Type: SNP
Chromosome: chr06	Position: 11856752
Reference Allele: A	Alternative Allele: G
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: 268. )

Flanking Sequence (100 bp) in Reference Genome:

TTGACCTACGGGTGCGATAGGTGGAGTTGCCTGCACAACTGGTTGAGCATCAGTGATTAAGGTTCGATAGTTTGGAAAAACACCTCCTGGCAAGTAGACC[A/G]
GGCCTGTAGCCTGATGCTCAGCTATCGAGCCATCGTCTATCGTCTTCATCATGTTTGACAGTGTGTTGACTAATATCCCGGATTGATTGATCAAAGCATG

Reverse complement sequence

CATGCTTTGATCAATCAATCCGGGATATTAGTCAACACACTGTCAAACATGATGAAGACGATAGACGATGGCTCGATAGCTGAGCATCAGGCTACAGGCC[T/C]
GGTCTACTTGCCAGGAGGTGTTTTTCCAAACTATCGAACCTTAATCACTGATGCTCAACCAGTTGTGCAGGCAACTCCACCTATCGCACCCGTAGGTCAA

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	66.50%	31.70%	1.16%	0.59%	NA
All Indica	2759	94.20%	2.90%	1.99%	0.91%	NA
All Japonica	1512	11.40%	88.40%	0.00%	0.20%	NA
Aus	269	92.20%	7.80%	0.00%	0.00%	NA
Indica I	595	90.60%	3.90%	3.87%	1.68%	NA
Indica II	465	96.10%	3.00%	0.43%	0.43%	NA
Indica III	913	96.40%	1.10%	1.64%	0.88%	NA
Indica Intermediate	786	93.10%	4.30%	1.91%	0.64%	NA
Temperate Japonica	767	3.40%	96.50%	0.00%	0.13%	NA
Tropical Japonica	504	24.00%	76.00%	0.00%	0.00%	NA
Japonica Intermediate	241	10.80%	88.40%	0.00%	0.83%	NA
VI/Aromatic	96	70.80%	29.20%	0.00%	0.00%	NA
Intermediate	90	62.20%	37.80%	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
vg0611856752	A -> G	LOC_Os06g20600.1	missense_variant ; p.Leu192Pro; MODERATE	nonsynonymous_codon ; L192P	Average:59.479; most accessible tissue: Minghui63 young leaf, score: 72.408	probably damaging	-2.029	TOLERATED	1.00
vg0611856752	A -> DEL	LOC_Os06g20600.1	N	frameshift_variant	Average:59.479; most accessible tissue: Minghui63 young leaf, score: 72.408	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0611856752	NA	5.61E-23	mr1020	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
vg0611856752	NA	2.42E-20	mr1021	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
vg0611856752	5.19E-08	5.19E-08	mr1032	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
vg0611856752	8.91E-07	8.91E-07	mr1165	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
vg0611856752	NA	1.45E-23	mr1477	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
vg0611856752	NA	1.14E-13	mr1478	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
vg0611856752	6.44E-09	6.44E-09	mr1478	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
vg0611856752	NA	6.38E-22	mr1971	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
vg0611856752	NA	5.26E-71	mr1087_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
vg0611856752	NA	3.64E-19	mr1165_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
vg0611856752	NA	3.39E-20	mr1276_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
vg0611856752	NA	3.16E-14	mr1333_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
vg0611856752	NA	7.34E-32	mr1477_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
vg0611856752	8.26E-06	8.26E-06	mr1477_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
vg0611856752	NA	2.24E-26	mr1617_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
vg0611856752	NA	1.51E-18	mr1637_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
vg0611856752	1.73E-06	NA	mr1733_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
vg0611856752	NA	2.76E-07	mr1837_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