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Detailed information for vg0122647957:

Variant ID: vg0122647957 (JBrowse)	Variation Type: SNP
Chromosome: chr01	Position: 22647957
Reference Allele: T	Alternative Allele: C
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

AATACCTCTAGTATGAATTTGTTCGAGCAATTGGATTCATTATGTTTAGACAGTACTCCCTCCGTTTCACAATGTAAGTCATTCTAGTATTTCCCACATT[T/C]
ATATTGATGTTAATGAATCTAGACATATATATCTATCTAGATTCATTAACATCAATATGAATGTGGGAAATGATAGAATGACTTACATTGTGAAACGGAG

Reverse complement sequence

CTCCGTTTCACAATGTAAGTCATTCTATCATTTCCCACATTCATATTGATGTTAATGAATCTAGATAGATATATATGTCTAGATTCATTAACATCAATAT[A/G]
AATGTGGGAAATACTAGAATGACTTACATTGTGAAACGGAGGGAGTACTGTCTAAACATAATGAATCCAATTGCTCGAACAAATTCATACTAGAGGTATT

Allele Frequencies:

Populations	Population Size	Frequency of T(primary allele)	Frequency of C(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	90.40%	9.50%	0.02%	0.00%	NA
All Indica	2759	88.00%	12.00%	0.04%	0.00%	NA
All Japonica	1512	93.80%	6.20%	0.00%	0.00%	NA
Aus	269	95.20%	4.80%	0.00%	0.00%	NA
Indica I	595	97.80%	2.20%	0.00%	0.00%	NA
Indica II	465	97.60%	2.40%	0.00%	0.00%	NA
Indica III	913	77.50%	22.50%	0.00%	0.00%	NA
Indica Intermediate	786	86.90%	13.00%	0.13%	0.00%	NA
Temperate Japonica	767	99.90%	0.10%	0.00%	0.00%	NA
Tropical Japonica	504	82.30%	17.70%	0.00%	0.00%	NA
Japonica Intermediate	241	98.80%	1.20%	0.00%	0.00%	NA
VI/Aromatic	96	99.00%	1.00%	0.00%	0.00%	NA
Intermediate	90	85.60%	14.40%	0.00%	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
vg0122647957	T -> C	LOC_Os01g40160.1	downstream_gene_variant ; 3129.0bp to feature; MODIFIER	silent_mutation	Average:32.344; most accessible tissue: Zhenshan97 panicle, score: 52.263	N	N	N	N
vg0122647957	T -> C	LOC_Os01g40150.1	intron_variant ; MODIFIER	silent_mutation	Average:32.344; most accessible tissue: Zhenshan97 panicle, score: 52.263	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0122647957	4.63E-07	4.63E-07	mr1778	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