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Detailed information for vg0722270556:

Variant ID: vg0722270556 (JBrowse)	Variation Type: SNP
Chromosome: chr07	Position: 22270556
Reference Allele: G	Alternative Allele: A
Primary Allele: A	Secondary Allele: G

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 1.00, G: 0.00, others allele: 0.00, population size: 191. )

Flanking Sequence (100 bp) in Reference Genome:

AATTGTGGTAGCATATAACGTTATGAAATTAATCTTAATAGGAAATCTAGTAATACAGTTTTCAATATTTTGTACATCAAATCTAGATCTAAACTGATAA[G/A]
AAAATCAGATTCCAATACATGAAAATGCCTATACAGTACAAAGGGTGACTACTTCGAGCAAAGATTAGCCTATTGAAGAAGTCACGTTCTGAAACCAAAG

Reverse complement sequence

CTTTGGTTTCAGAACGTGACTTCTTCAATAGGCTAATCTTTGCTCGAAGTAGTCACCCTTTGTACTGTATAGGCATTTTCATGTATTGGAATCTGATTTT[C/T]
TTATCAGTTTAGATCTAGATTTGATGTACAAAATATTGAAAACTGTATTACTAGATTTCCTATTAAGATTAATTTCATAACGTTATATGCTACCACAATT

Allele Frequencies:

Populations	Population Size	Frequency of A(primary allele)	Frequency of G(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	62.50%	37.30%	0.17%	0.00%	NA
All Indica	2759	95.50%	4.30%	0.14%	0.00%	NA
All Japonica	1512	7.40%	92.60%	0.00%	0.00%	NA
Aus	269	51.70%	48.30%	0.00%	0.00%	NA
Indica I	595	99.70%	0.20%	0.17%	0.00%	NA
Indica II	465	94.00%	6.00%	0.00%	0.00%	NA
Indica III	913	98.50%	1.40%	0.11%	0.00%	NA
Indica Intermediate	786	89.90%	9.80%	0.25%	0.00%	NA
Temperate Japonica	767	2.10%	97.90%	0.00%	0.00%	NA
Tropical Japonica	504	14.30%	85.70%	0.00%	0.00%	NA
Japonica Intermediate	241	10.00%	90.00%	0.00%	0.00%	NA
VI/Aromatic	96	26.00%	72.90%	1.04%	0.00%	NA
Intermediate	90	45.60%	51.10%	3.33%	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
vg0722270556	G -> A	LOC_Os07g37180.1	intron_variant ; MODIFIER	silent_mutation	Average:44.485; most accessible tissue: Callus, score: 80.034	N	N	N	N
vg0722270556	G -> A	LOC_Os07g37180.2	intron_variant ; MODIFIER	silent_mutation	Average:44.485; most accessible tissue: Callus, score: 80.034	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0722270556	NA	4.39E-07	mr1082	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
vg0722270556	NA	2.30E-31	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
vg0722270556	NA	3.36E-08	mr1226	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
vg0722270556	NA	1.18E-11	mr1233	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
vg0722270556	NA	5.91E-25	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
vg0722270556	NA	4.26E-07	mr1411	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
vg0722270556	NA	2.05E-16	mr1484	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
vg0722270556	NA	2.12E-07	mr1613	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
vg0722270556	NA	1.17E-08	mr1644	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
vg0722270556	NA	4.02E-06	mr1913	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
vg0722270556	NA	4.68E-16	mr1949	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
vg0722270556	NA	8.13E-07	mr1949	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
vg0722270556	NA	5.20E-32	mr1085_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
vg0722270556	NA	5.27E-38	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
vg0722270556	NA	2.03E-37	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
vg0722270556	6.13E-06	2.14E-29	mr1233_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
vg0722270556	NA	4.41E-06	mr1233_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
vg0722270556	NA	1.86E-51	mr1404_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
vg0722270556	NA	5.84E-06	mr1613_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
vg0722270556	7.93E-06	3.06E-27	mr1949_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