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Detailed information for vg0418071751:

Variant ID: vg0418071751 (JBrowse)	Variation Type: SNP
Chromosome: chr04	Position: 18071751
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: 309. )

Flanking Sequence (100 bp) in Reference Genome:

CTCTCGCTAGTCATTATTAAGCACTGGCTTGCTAGAGTTGCCAGATCACTTATCAATCCCATGTTATCTTCGTGCAATATTTCTGCGTCTATGAGCTCAA[G/A]
GAAGTGGCCTTCTCTCATGGCCTCTTGAAATATTAACGCGAGGCTGACCTTATCCACGGATAATGGCATTCGCCGGGTTAAGAGCTCAAGAAGAACTATA

Reverse complement sequence

TATAGTTCTTCTTGAGCTCTTAACCCGGCGAATGCCATTATCCGTGGATAAGGTCAGCCTCGCGTTAATATTTCAAGAGGCCATGAGAGAAGGCCACTTC[C/T]
TTGAGCTCATAGACGCAGAAATATTGCACGAAGATAACATGGGATTGATAAGTGATCTGGCAACTCTAGCAAGCCAGTGCTTAATAATGACTAGCGAGAG

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	89.80%	0.30%	1.31%	8.59%	NA
All Indica	2759	98.90%	0.00%	0.33%	0.72%	NA
All Japonica	1512	72.00%	0.60%	2.98%	24.40%	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	95.70%	0.20%	1.29%	2.80%	NA
Indica III	913	99.90%	0.00%	0.00%	0.11%	NA
Indica Intermediate	786	98.90%	0.00%	0.38%	0.76%	NA
Temperate Japonica	767	98.20%	0.00%	0.13%	1.69%	NA
Tropical Japonica	504	39.30%	1.20%	6.55%	52.98%	NA
Japonica Intermediate	241	57.30%	1.20%	4.56%	36.93%	NA
VI/Aromatic	96	83.30%	2.10%	6.25%	8.33%	NA
Intermediate	90	87.80%	0.00%	2.22%	10.00%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0418071751	G -> DEL	LOC_Os04g30270.1	N	frameshift_variant	Average:66.334; most accessible tissue: Zhenshan97 young leaf, score: 91.83	N	N	N	N
vg0418071751	G -> A	LOC_Os04g30270.1	missense_variant ; p.Leu273Phe; MODERATE	nonsynonymous_codon ; L273F	Average:66.334; most accessible tissue: Zhenshan97 young leaf, score: 91.83	probably damaging	2.028	TOLERATED	0.81

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0418071751	5.39E-09	NA	mr1076	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
vg0418071751	2.24E-07	NA	mr1082	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
vg0418071751	NA	2.13E-06	mr1082	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
vg0418071751	1.61E-06	NA	mr1083	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
vg0418071751	NA	7.13E-06	mr1083	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
vg0418071751	2.08E-08	NA	mr1104	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
vg0418071751	7.51E-07	NA	mr1107	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
vg0418071751	NA	5.05E-07	mr1220	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
vg0418071751	2.97E-10	NA	mr1226	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
vg0418071751	NA	3.66E-06	mr1226	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
vg0418071751	NA	1.07E-06	mr1408	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
vg0418071751	1.63E-06	NA	mr1411	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
vg0418071751	NA	6.72E-06	mr1448	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
vg0418071751	1.65E-07	NA	mr1104_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
vg0418071751	1.13E-06	NA	mr1107_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
vg0418071751	3.44E-06	NA	mr1226_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
vg0418071751	NA	1.70E-06	mr1498_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
vg0418071751	NA	6.39E-08	mr1502_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
vg0418071751	NA	1.15E-06	mr1870_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