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Detailed information for vg0233556355:

Variant ID: vg0233556355 (JBrowse)	Variation Type: SNP
Chromosome: chr02	Position: 33556355
Reference Allele: G	Alternative Allele: T
Primary Allele: G	Secondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

CATCAAACAATTGTTCTGGGATTCTGCCCAACAAGGCATTTCCCTGCAGGTACCTTGGGATCTTGGGGGCATTAATCTGGCGAGTCAGTTGCATCGGCTT[G/T]
GGGACAAGCCGATTCTTAACGGGGGAAGAATGTCATGTACATGGCCTGCTGTGATGTCTTTCCAGGAGGCTAGACAAGTGGGCTGGCTTTGGGCCCATTC

Reverse complement sequence

GAATGGGCCCAAAGCCAGCCCACTTGTCTAGCCTCCTGGAAAGACATCACAGCAGGCCATGTACATGACATTCTTCCCCCGTTAAGAATCGGCTTGTCCC[C/A]
AAGCCGATGCAACTGACTCGCCAGATTAATGCCCCCAAGATCCCAAGGTACCTGCAGGGAAATGCCTTGTTGGGCAGAATCCCAGAACAATTGTTTGATG

Allele Frequencies:

Populations	Population Size	Frequency of G(primary allele)	Frequency of T(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	98.60%	0.00%	1.08%	0.32%	NA
All Indica	2759	99.90%	0.10%	0.04%	0.00%	NA
All Japonica	1512	96.40%	0.00%	2.91%	0.66%	NA
Aus	269	100.00%	0.00%	0.00%	0.00%	NA
Indica I	595	99.80%	0.00%	0.17%	0.00%	NA
Indica II	465	99.80%	0.20%	0.00%	0.00%	NA
Indica III	913	100.00%	0.00%	0.00%	0.00%	NA
Indica Intermediate	786	99.90%	0.10%	0.00%	0.00%	NA
Temperate Japonica	767	93.50%	0.00%	5.35%	1.17%	NA
Tropical Japonica	504	99.80%	0.00%	0.20%	0.00%	NA
Japonica Intermediate	241	98.80%	0.00%	0.83%	0.41%	NA
VI/Aromatic	96	91.70%	0.00%	5.21%	3.12%	NA
Intermediate	90	96.70%	0.00%	1.11%	2.22%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0233556355	G -> T	LOC_Os02g54790.1	intron_variant ; MODIFIER	silent_mutation	Average:55.941; most accessible tissue: Zhenshan97 panicle, score: 77.482	N	N	N	N
vg0233556355	G -> DEL	N	N	silent_mutation	Average:55.941; most accessible tissue: Zhenshan97 panicle, score: 77.482	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0233556355	9.86E-07	NA	mr1588_2	Jap_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