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Detailed information for vg0722461551:

Variant ID: vg0722461551 (JBrowse)	Variation Type: SNP
Chromosome: chr07	Position: 22461551
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.97, A: 0.03, others allele: 0.00, population size: 241. )

Flanking Sequence (100 bp) in Reference Genome:

CAAGGATACGTAGTACGACATCAAGCAAACAACAAAAGACAGATTATACTGGTTCAGGCCGGTAGGTAATAGCCCTAATCCAGTTGGTATGGAATTATAC[G/A]
ATGAAAATCATAGATTACAAAGGGAATAACAGAACTTGATGATACCGATGAGACCGTAGTCGAGTTGGTTCGACTAGATCACCCGGCAACTTAGCTCCTG

Reverse complement sequence

CAGGAGCTAAGTTGCCGGGTGATCTAGTCGAACCAACTCGACTACGGTCTCATCGGTATCATCAAGTTCTGTTATTCCCTTTGTAATCTATGATTTTCAT[C/T]
GTATAATTCCATACCAACTGGATTAGGGCTATTACCTACCGGCCTGAACCAGTATAATCTGTCTTTTGTTGTTTGCTTGATGTCGTACTACGTATCCTTG

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	63.10%	36.40%	0.15%	0.32%	NA
All Indica	2759	80.80%	18.60%	0.11%	0.54%	NA
All Japonica	1512	37.60%	62.20%	0.20%	0.00%	NA
Aus	269	16.40%	83.60%	0.00%	0.00%	NA
Indica I	595	99.20%	0.70%	0.17%	0.00%	NA
Indica II	465	72.50%	27.50%	0.00%	0.00%	NA
Indica III	913	71.10%	27.20%	0.22%	1.53%	NA
Indica Intermediate	786	83.10%	16.80%	0.00%	0.13%	NA
Temperate Japonica	767	53.80%	45.80%	0.39%	0.00%	NA
Tropical Japonica	504	23.60%	76.40%	0.00%	0.00%	NA
Japonica Intermediate	241	14.90%	85.10%	0.00%	0.00%	NA
VI/Aromatic	96	96.90%	3.10%	0.00%	0.00%	NA
Intermediate	90	55.60%	43.30%	1.11%	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
vg0722461551	G -> DEL	N	N	silent_mutation	Average:48.338; most accessible tissue: Minghui63 panicle, score: 59.629	N	N	N	N
vg0722461551	G -> A	LOC_Os07g37510.1	upstream_gene_variant ; 3022.0bp to feature; MODIFIER	silent_mutation	Average:48.338; most accessible tissue: Minghui63 panicle, score: 59.629	N	N	N	N
vg0722461551	G -> A	LOC_Os07g37520.1	downstream_gene_variant ; 4098.0bp to feature; MODIFIER	silent_mutation	Average:48.338; most accessible tissue: Minghui63 panicle, score: 59.629	N	N	N	N
vg0722461551	G -> A	LOC_Os07g37510-LOC_Os07g37520	intergenic_region ; MODIFIER	silent_mutation	Average:48.338; most accessible tissue: Minghui63 panicle, score: 59.629	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0722461551	NA	2.91E-08	mr1163	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
vg0722461551	NA	7.08E-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
vg0722461551	NA	1.20E-06	mr1236	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
vg0722461551	8.25E-06	NA	mr1343	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
vg0722461551	NA	5.46E-09	mr1354	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
vg0722461551	NA	3.00E-15	mr1531	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
vg0722461551	NA	8.52E-06	mr1679	Ind_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
vg0722461551	NA	3.92E-09	mr1829	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
vg0722461551	3.25E-06	NA	mr1902	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
vg0722461551	NA	1.87E-06	mr1011_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
vg0722461551	NA	2.60E-06	mr1078_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
vg0722461551	NA	2.42E-07	mr1188_2	Ind_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
vg0722461551	NA	8.19E-09	mr1220_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
vg0722461551	NA	7.12E-07	mr1236_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
vg0722461551	NA	7.77E-07	mr1405_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
vg0722461551	NA	5.44E-07	mr1668_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
vg0722461551	NA	1.71E-06	mr1863_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