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Detailed information for vg1124617651:

Variant ID: vg1124617651 (JBrowse)	Variation Type: SNP
Chromosome: chr11	Position: 24617651
Reference Allele: C	Alternative Allele: A
Primary Allele: C	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

TAGCATACCTTCCGAGATAGAAAAACTCAGTAGCCTCAGTGTCCTTCAAATGGATAGAAATTTTCTTTCTGGCCAAATTCCTGACACACTAGTAAATCTT[C/A]
AAAACTTGTCAATCCTAAGTTTGTCCAACAACAAGCTTTCTGGAGAGATCCCACGATCAATTGGAAAATTAGAGCAGCTTACTAAACTTTATCTTCAGGA

Reverse complement sequence

TCCTGAAGATAAAGTTTAGTAAGCTGCTCTAATTTTCCAATTGATCGTGGGATCTCTCCAGAAAGCTTGTTGTTGGACAAACTTAGGATTGACAAGTTTT[G/T]
AAGATTTACTAGTGTGTCAGGAATTTGGCCAGAAAGAAAATTTCTATCCATTTGAAGGACACTGAGGCTACTGAGTTTTTCTATCTCGGAAGGTATGCTA

Allele Frequencies:

Populations	Population Size	Frequency of C(primary allele)	Frequency of A(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	45.90%	15.90%	1.21%	37.01%	NA
All Indica	2759	46.60%	2.50%	0.98%	49.91%	NA
All Japonica	1512	52.10%	33.10%	1.39%	13.43%	NA
Aus	269	15.20%	55.80%	2.23%	26.77%	NA
Indica I	595	58.70%	3.70%	0.67%	36.97%	NA
Indica II	465	17.40%	0.90%	0.43%	81.29%	NA
Indica III	913	53.80%	2.00%	0.88%	43.37%	NA
Indica Intermediate	786	46.60%	3.10%	1.65%	48.73%	NA
Temperate Japonica	767	59.50%	29.20%	1.56%	9.78%	NA
Tropical Japonica	504	48.40%	31.30%	0.99%	19.25%	NA
Japonica Intermediate	241	36.50%	49.00%	1.66%	12.86%	NA
VI/Aromatic	96	15.60%	17.70%	0.00%	66.67%	NA
Intermediate	90	42.20%	17.80%	3.33%	36.67%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1124617651	C -> A	LOC_Os11g41100.1	missense_variant ; p.Gln513Lys; MODERATE	nonsynonymous_codon ; Q513K	Average:19.126; most accessible tissue: Zhenshan97 flower, score: 45.926	benign	0.048	TOLERATED	0.76
vg1124617651	C -> DEL	LOC_Os11g41100.1	N	frameshift_variant	Average:19.126; most accessible tissue: Zhenshan97 flower, score: 45.926	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1124617651	NA	6.88E-10	mr1465	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
vg1124617651	NA	9.64E-08	mr1666	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
vg1124617651	NA	3.89E-07	mr1041_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
vg1124617651	NA	2.42E-06	mr1263_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
vg1124617651	NA	2.12E-06	mr1294_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
vg1124617651	NA	7.21E-08	mr1302_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
vg1124617651	NA	1.23E-06	mr1488_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
vg1124617651	NA	1.14E-08	mr1604_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
vg1124617651	NA	4.91E-07	mr1729_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
vg1124617651	NA	4.47E-09	mr1751_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
vg1124617651	9.84E-06	9.75E-08	mr1813_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
vg1124617651	NA	1.12E-07	mr1824_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
vg1124617651	2.60E-06	4.65E-06	mr1854_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
vg1124617651	NA	2.22E-07	mr1894_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