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Detailed information for vg0123635868:

Variant ID: vg0123635868 (JBrowse)	Variation Type: SNP
Chromosome: chr01	Position: 23635868
Reference Allele: C	Alternative Allele: A
Primary Allele: C	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

AAGTTTATGTGTATAGGAAAGTTTTGATGTGATGAAAAAGTTGGAAGTTTGAAGAAAAAATTTGGAACTAAACAAGGCCCGAGTATGAGGGGATGTGTGA[C/A]
CCGGTGGGGGAAGCGAATTTCCTTTAAGGTTTCTGAACAATTCTTTGACTAAAGGAGAAACAAAAATATTACTTCCTCCGTTTTAGATTATAAGACGTTT

Reverse complement sequence

AAACGTCTTATAATCTAAAACGGAGGAAGTAATATTTTTGTTTCTCCTTTAGTCAAAGAATTGTTCAGAAACCTTAAAGGAAATTCGCTTCCCCCACCGG[G/T]
TCACACATCCCCTCATACTCGGGCCTTGTTTAGTTCCAAATTTTTTCTTCAAACTTCCAACTTTTTCATCACATCAAAACTTTCCTATACACATAAACTT

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	81.80%	9.50%	8.34%	0.34%	NA
All Indica	2759	92.90%	6.50%	0.58%	0.00%	NA
All Japonica	1512	57.70%	16.80%	24.40%	1.06%	NA
Aus	269	95.90%	4.10%	0.00%	0.00%	NA
Indica I	595	98.30%	1.70%	0.00%	0.00%	NA
Indica II	465	97.20%	1.90%	0.86%	0.00%	NA
Indica III	913	86.30%	13.10%	0.55%	0.00%	NA
Indica Intermediate	786	93.90%	5.20%	0.89%	0.00%	NA
Temperate Japonica	767	51.50%	25.80%	21.12%	1.56%	NA
Tropical Japonica	504	62.90%	1.00%	35.32%	0.79%	NA
Japonica Intermediate	241	66.80%	21.20%	12.03%	0.00%	NA
VI/Aromatic	96	95.80%	1.00%	3.12%	0.00%	NA
Intermediate	90	91.10%	2.20%	6.67%	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
vg0123635868	C -> A	LOC_Os01g41750.1	upstream_gene_variant ; 493.0bp to feature; MODIFIER	silent_mutation	Average:31.307; most accessible tissue: Zhenshan97 flower, score: 59.755	N	N	N	N
vg0123635868	C -> A	LOC_Os01g41740.1	downstream_gene_variant ; 4631.0bp to feature; MODIFIER	silent_mutation	Average:31.307; most accessible tissue: Zhenshan97 flower, score: 59.755	N	N	N	N
vg0123635868	C -> A	LOC_Os01g41760.1	downstream_gene_variant ; 1374.0bp to feature; MODIFIER	silent_mutation	Average:31.307; most accessible tissue: Zhenshan97 flower, score: 59.755	N	N	N	N
vg0123635868	C -> A	LOC_Os01g41770.1	downstream_gene_variant ; 3786.0bp to feature; MODIFIER	silent_mutation	Average:31.307; most accessible tissue: Zhenshan97 flower, score: 59.755	N	N	N	N
vg0123635868	C -> A	LOC_Os01g41750-LOC_Os01g41760	intergenic_region ; MODIFIER	silent_mutation	Average:31.307; most accessible tissue: Zhenshan97 flower, score: 59.755	N	N	N	N
vg0123635868	C -> DEL	N	N	silent_mutation	Average:31.307; most accessible tissue: Zhenshan97 flower, score: 59.755	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0123635868	8.88E-06	8.87E-06	mr1766_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
vg0123635868	1.30E-07	NA	mr1970_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