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Detailed information for vg0100619901:

Variant ID: vg0100619901 (JBrowse)	Variation Type: SNP
Chromosome: chr01	Position: 619901
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

ATTCCGAATTTTAGCTATTTTTAGATTGTATTTCTACTTGGACTCTCCTTTTCGTTTTTTCTTTTTCTCCTATTAATGTGGGAATTTCTAGCCCCCACAG[C/T]
GAACGTGGTGCCTTCTTTCAAAGCTGTATTTTATTATAAATTAAATTTTAGTTGTTAAAAATAATATCATTGGATATTCATTTAAATTTAATTTTATATG

Reverse complement sequence

CATATAAAATTAAATTTAAATGAATATCCAATGATATTATTTTTAACAACTAAAATTTAATTTATAATAAAATACAGCTTTGAAAGAAGGCACCACGTTC[G/A]
CTGTGGGGGCTAGAAATTCCCACATTAATAGGAGAAAAAGAAAAAACGAAAAGGAGAGTCCAAGTAGAAATACAATCTAAAAATAGCTAAAATTCGGAAT

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	97.80%	0.10%	1.02%	1.04%	NA
All Indica	2759	96.50%	0.10%	1.70%	1.70%	NA
All Japonica	1512	99.90%	0.00%	0.00%	0.07%	NA
Aus	269	98.90%	1.10%	0.00%	0.00%	NA
Indica I	595	100.00%	0.00%	0.00%	0.00%	NA
Indica II	465	90.80%	0.20%	3.66%	5.38%	NA
Indica III	913	97.90%	0.10%	1.10%	0.88%	NA
Indica Intermediate	786	95.70%	0.00%	2.54%	1.78%	NA
Temperate Japonica	767	99.90%	0.00%	0.00%	0.13%	NA
Tropical Japonica	504	100.00%	0.00%	0.00%	0.00%	NA
Japonica Intermediate	241	100.00%	0.00%	0.00%	0.00%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	97.80%	0.00%	1.11%	1.11%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0100619901	C -> T	LOC_Os01g02139.1	upstream_gene_variant ; 4186.0bp to feature; MODIFIER	silent_mutation	Average:13.984; most accessible tissue: Zhenshan97 panicle, score: 28.447	N	N	N	N
vg0100619901	C -> T	LOC_Os01g02120.1	downstream_gene_variant ; 4251.0bp to feature; MODIFIER	silent_mutation	Average:13.984; most accessible tissue: Zhenshan97 panicle, score: 28.447	N	N	N	N
vg0100619901	C -> T	LOC_Os01g02130.1	downstream_gene_variant ; 671.0bp to feature; MODIFIER	silent_mutation	Average:13.984; most accessible tissue: Zhenshan97 panicle, score: 28.447	N	N	N	N
vg0100619901	C -> T	LOC_Os01g02120-LOC_Os01g02130	intergenic_region ; MODIFIER	silent_mutation	Average:13.984; most accessible tissue: Zhenshan97 panicle, score: 28.447	N	N	N	N
vg0100619901	C -> DEL	N	N	silent_mutation	Average:13.984; most accessible tissue: Zhenshan97 panicle, score: 28.447	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0100619901	4.19E-06	4.19E-06	mr1992	Ind_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