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Detailed information for vg0123775896:

Variant ID: vg0123775896 (JBrowse)	Variation Type: SNP
Chromosome: chr01	Position: 23775896
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

AAAATCTCAATGAGTGAAATAGCTTAGATCGTAAGAATACTCACAAATTAATGCATACCCTAGAGTTTTTTTTTTTGAAATACACAAAAGACTTGCATAT[C/T]
ATTGCATTAAGAGGAGTAAAGTAATACAAGACAGACAGAGAAGAACAGGGAGGAGAGAGGAGGGGAGGAGAAAAGGAGAAACGGAAAAAGACACACTAAA

Reverse complement sequence

TTTAGTGTGTCTTTTTCCGTTTCTCCTTTTCTCCTCCCCTCCTCTCTCCTCCCTGTTCTTCTCTGTCTGTCTTGTATTACTTTACTCCTCTTAATGCAAT[G/A]
ATATGCAAGTCTTTTGTGTATTTCAAAAAAAAAAACTCTAGGGTATGCATTAATTTGTGAGTATTCTTACGATCTAAGCTATTTCACTCATTGAGATTTT

Allele Frequencies:

Populations	Population Size	Frequency of C(primary allele)	Frequency of T(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	28.30%	15.90%	0.55%	55.25%	NA
All Indica	2759	3.50%	7.20%	0.80%	88.55%	NA
All Japonica	1512	79.00%	13.40%	0.07%	7.61%	NA
Aus	269	1.90%	90.30%	0.00%	7.81%	NA
Indica I	595	3.90%	0.50%	0.50%	95.13%	NA
Indica II	465	3.70%	3.40%	0.86%	92.04%	NA
Indica III	913	0.80%	10.70%	0.66%	87.84%	NA
Indica Intermediate	786	6.20%	10.30%	1.15%	82.32%	NA
Temperate Japonica	767	99.20%	0.40%	0.00%	0.39%	NA
Tropical Japonica	504	47.20%	32.30%	0.20%	20.24%	NA
Japonica Intermediate	241	80.90%	14.90%	0.00%	4.15%	NA
VI/Aromatic	96	8.30%	90.60%	0.00%	1.04%	NA
Intermediate	90	40.00%	22.20%	3.33%	34.44%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0123775896	C -> T	LOC_Os01g41930.1	5_prime_UTR_variant ; 606.0bp to feature; MODIFIER	silent_mutation	Average:10.918; most accessible tissue: Callus, score: 62.341	N	N	N	N
vg0123775896	C -> T	LOC_Os01g41920.1	upstream_gene_variant ; 3213.0bp to feature; MODIFIER	silent_mutation	Average:10.918; most accessible tissue: Callus, score: 62.341	N	N	N	N
vg0123775896	C -> T	LOC_Os01g41910.1	downstream_gene_variant ; 4381.0bp to feature; MODIFIER	silent_mutation	Average:10.918; most accessible tissue: Callus, score: 62.341	N	N	N	N
vg0123775896	C -> DEL	N	N	silent_mutation	Average:10.918; most accessible tissue: Callus, score: 62.341	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0123775896	NA	3.20E-06	mr1227	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
vg0123775896	NA	1.25E-06	mr1082_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