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Detailed information for vg0122291977:

Variant ID: vg0122291977 (JBrowse)	Variation Type: SNP
Chromosome: chr01	Position: 22291977
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

CTCCCTCTCCAACGCTACTCTCTCCCTCTCCGGCGTCTCACCCTCTTCCTCTCCCTCTCTAGCTCCTCTCCCTCTGGGTACCACACGCTCCCTCTCCATC[C/T]
GGCGCCGCTCACTCTTCCTCTCCGACGCGCTCTAGTGACGAGGGAGAGGAGCTGGCGGCCAGTCCTAGGTGACCCCGATCTCGGCGAAGGCAGGTGGCTC

Reverse complement sequence

GAGCCACCTGCCTTCGCCGAGATCGGGGTCACCTAGGACTGGCCGCCAGCTCCTCTCCCTCGTCACTAGAGCGCGTCGGAGAGGAAGAGTGAGCGGCGCC[G/A]
GATGGAGAGGGAGCGTGTGGTACCCAGAGGGAGAGGAGCTAGAGAGGGAGAGGAAGAGGGTGAGACGCCGGAGAGGGAGAGAGTAGCGTTGGAGAGGGAG

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	85.70%	12.10%	0.11%	2.14%	NA
All Indica	2759	80.80%	17.10%	0.04%	1.99%	NA
All Japonica	1512	97.20%	0.20%	0.20%	2.45%	NA
Aus	269	97.80%	2.20%	0.00%	0.00%	NA
Indica I	595	97.30%	2.00%	0.17%	0.50%	NA
Indica II	465	97.40%	1.10%	0.00%	1.51%	NA
Indica III	913	61.10%	35.70%	0.00%	3.18%	NA
Indica Intermediate	786	81.40%	16.50%	0.00%	2.04%	NA
Temperate Japonica	767	96.00%	0.00%	0.39%	3.65%	NA
Tropical Japonica	504	100.00%	0.00%	0.00%	0.00%	NA
Japonica Intermediate	241	95.00%	1.20%	0.00%	3.73%	NA
VI/Aromatic	96	13.50%	78.10%	0.00%	8.33%	NA
Intermediate	90	83.30%	14.40%	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
vg0122291977	C -> T	LOC_Os01g39550.1	upstream_gene_variant ; 3756.0bp to feature; MODIFIER	silent_mutation	Average:75.806; most accessible tissue: Zhenshan97 young leaf, score: 90.456	N	N	N	N
vg0122291977	C -> T	LOC_Os01g39540-LOC_Os01g39550	intergenic_region ; MODIFIER	silent_mutation	Average:75.806; most accessible tissue: Zhenshan97 young leaf, score: 90.456	N	N	N	N
vg0122291977	C -> DEL	N	N	silent_mutation	Average:75.806; most accessible tissue: Zhenshan97 young leaf, score: 90.456	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0122291977	NA	1.57E-06	mr1561_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
vg0122291977	NA	1.91E-06	mr1908_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
vg0122291977	NA	1.58E-06	mr1994_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