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Detailed information for vg0108024813:

Variant ID: vg0108024813 (JBrowse)	Variation Type: SNP
Chromosome: chr01	Position: 8024813
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

GGTAGTTGTCGATGGCCTTGCGGTCCGGGGCGATGCGGCGGGGCACGGTGATGCGGGAGGCGAACGGAGGGGCGCCGAAGTTTAACCGGAGCTCGGTGCC[C/T]
GGAGGAAAGTGGAACTCGTCGTGGGCAACGTGCGGGACGGAGACGAGGATCACCCACCACCCCTTCGCCGCCTCCCTCATCTGCATCTCCTCCGCCGCCC

Reverse complement sequence

GGGCGGCGGAGGAGATGCAGATGAGGGAGGCGGCGAAGGGGTGGTGGGTGATCCTCGTCTCCGTCCCGCACGTTGCCCACGACGAGTTCCACTTTCCTCC[G/A]
GGCACCGAGCTCCGGTTAAACTTCGGCGCCCCTCCGTTCGCCTCCCGCATCACCGTGCCCCGCCGCATCGCCCCGGACCGCAAGGCCATCGACAACTACC

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	97.70%	2.30%	0.00%	0.00%	NA
All Indica	2759	100.00%	0.00%	0.00%	0.00%	NA
All Japonica	1512	92.90%	7.10%	0.00%	0.00%	NA
Aus	269	100.00%	0.00%	0.00%	0.00%	NA
Indica I	595	100.00%	0.00%	0.00%	0.00%	NA
Indica II	465	100.00%	0.00%	0.00%	0.00%	NA
Indica III	913	100.00%	0.00%	0.00%	0.00%	NA
Indica Intermediate	786	100.00%	0.00%	0.00%	0.00%	NA
Temperate Japonica	767	87.70%	12.30%	0.00%	0.00%	NA
Tropical Japonica	504	100.00%	0.00%	0.00%	0.00%	NA
Japonica Intermediate	241	94.20%	5.80%	0.00%	0.00%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	100.00%	0.00%	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
vg0108024813	C -> T	LOC_Os01g14320.1	synonymous_variant ; p.Pro41Pro; LOW	synonymous_codon	Average:73.519; most accessible tissue: Zhenshan97 young leaf, score: 86.852	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0108024813	7.60E-06	7.60E-06	mr1480	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