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Detailed information for vg0502041473:

Variant ID: vg0502041473 (JBrowse)	Variation Type: SNP
Chromosome: chr05	Position: 2041473
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.01, others allele: 0.00, population size: 204. )

Flanking Sequence (100 bp) in Reference Genome:

CGAGTGCTTTCTTCAGCTGGCGCACCTCTTCGTCTTCTTTCTGTCGATTTATGACGATGCCTGCAGGTTGCAAGTTGTCGTCCCACCAATTGATTAAGAT[G/A]
GGGGGACGAGAATCAGCAGTTGCCTTTATGCGAGAGATTTCTTCTCTGTCACCGGCCAGTGGTCCTGATGTATTTCCAGACATTAGGCAAGCAAATCGGA

Reverse complement sequence

TCCGATTTGCTTGCCTAATGTCTGGAAATACATCAGGACCACTGGCCGGTGACAGAGAAGAAATCTCTCGCATAAAGGCAACTGCTGATTCTCGTCCCCC[C/T]
ATCTTAATCAATTGGTGGGACGACAACTTGCAACCTGCAGGCATCGTCATAAATCGACAGAAAGAAGACGAAGAGGTGCGCCAGCTGAAGAAAGCACTCG

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	68.50%	0.10%	8.63%	22.70%	NA
All Indica	2759	55.70%	0.30%	13.85%	30.16%	NA
All Japonica	1512	87.10%	0.00%	0.86%	12.04%	NA
Aus	269	81.80%	0.00%	2.23%	15.99%	NA
Indica I	595	86.20%	0.20%	1.01%	12.61%	NA
Indica II	465	56.80%	0.20%	10.75%	32.26%	NA
Indica III	913	33.50%	0.40%	23.33%	42.72%	NA
Indica Intermediate	786	57.90%	0.10%	14.38%	27.61%	NA
Temperate Japonica	767	97.80%	0.00%	0.13%	2.09%	NA
Tropical Japonica	504	71.80%	0.00%	1.19%	26.98%	NA
Japonica Intermediate	241	85.10%	0.00%	2.49%	12.45%	NA
VI/Aromatic	96	94.80%	0.00%	2.08%	3.12%	NA
Intermediate	90	80.00%	0.00%	5.56%	14.44%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0502041473	G -> DEL	LOC_Os05g04430.1	N	frameshift_variant	Average:28.483; most accessible tissue: Zhenshan97 flag leaf, score: 56.01	N	N	N	N
vg0502041473	G -> A	LOC_Os05g04430.1	synonymous_variant ; p.Pro496Pro; LOW	synonymous_codon	Average:28.483; most accessible tissue: Zhenshan97 flag leaf, score: 56.01	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0502041473	5.88E-07	NA	mr1907_2	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