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Detailed information for vg1010265444:

Variant ID: vg1010265444 (JBrowse)	Variation Type: SNP
Chromosome: chr10	Position: 10265444
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

GGAGGATGATGTACCGCTTGTGCCATAGTATAATGGCGTGGCTTGTGTCTCGTAGATACGTCTCAACGTCTCCTCCTGGGTAGTCCAACTCGAGGTCCTC[G/A]
TACGCGGCTTCCACCAGCTCAACTTCGACCCTCGAGTATCCTGCTGGAATCGGCCTGCAGTGGTAAGTCCCAGAAGGGTCCGTTGGGATGGCCATTCCCG

Reverse complement sequence

CGGGAATGGCCATCCCAACGGACCCTTCTGGGACTTACCACTGCAGGCCGATTCCAGCAGGATACTCGAGGGTCGAAGTTGAGCTGGTGGAAGCCGCGTA[C/T]
GAGGACCTCGAGTTGGACTACCCAGGAGGAGACGTTGAGACGTATCTACGAGACACAAGCCACGCCATTATACTATGGCACAAGCGGTACATCATCCTCC

Allele Frequencies:

Populations	Population Size	Frequency of G(primary allele)	Frequency of A(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	55.30%	43.50%	1.16%	0.00%	NA
All Indica	2759	39.70%	59.50%	0.83%	0.00%	NA
All Japonica	1512	86.20%	13.40%	0.40%	0.00%	NA
Aus	269	24.90%	65.80%	9.29%	0.00%	NA
Indica I	595	24.40%	74.50%	1.18%	0.00%	NA
Indica II	465	51.60%	47.30%	1.08%	0.00%	NA
Indica III	913	48.50%	51.00%	0.44%	0.00%	NA
Indica Intermediate	786	34.00%	65.10%	0.89%	0.00%	NA
Temperate Japonica	767	91.10%	8.70%	0.13%	0.00%	NA
Tropical Japonica	504	79.60%	19.40%	0.99%	0.00%	NA
Japonica Intermediate	241	84.60%	15.40%	0.00%	0.00%	NA
VI/Aromatic	96	91.70%	8.30%	0.00%	0.00%	NA
Intermediate	90	66.70%	32.20%	1.11%	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
vg1010265444	G -> A	LOC_Os10g20410.1	synonymous_variant ; p.Tyr307Tyr; LOW	synonymous_codon	Average:43.629; most accessible tissue: Minghui63 young leaf, score: 83.166	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1010265444	2.28E-06	NA	mr1274	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