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Detailed information for vg0726119227:

Variant ID: vg0726119227 (JBrowse)	Variation Type: SNP
Chromosome: chr07	Position: 26119227
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, others allele: 0.00, population size: 120. )

Flanking Sequence (100 bp) in Reference Genome:

GACTTAATGATGAGCTTTCTTACCCACTCATGACTGGGGATTATCCTGATTTCCAGAAGTTAGTGGATAAGGCTATTCGCCAGGAGGACAAGTACAACCG[C/T]
ATGGAACAGAAGAAACGCCGGATTGCTTACTTCAAGGCACAACAGGGGAATAGTCAGAGGCCGCGTCTTACTTTAGGACCCCAGTCCATGCCACAGGGAG

Reverse complement sequence

CTCCCTGTGGCATGGACTGGGGTCCTAAAGTAAGACGCGGCCTCTGACTATTCCCCTGTTGTGCCTTGAAGTAAGCAATCCGGCGTTTCTTCTGTTCCAT[G/A]
CGGTTGTACTTGTCCTCCTGGCGAATAGCCTTATCCACTAACTTCTGGAAATCAGGATAATCCCCAGTCATGAGTGGGTAAGAAAGCTCATCATTAAGTC

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	94.20%	0.10%	4.66%	1.06%	NA
All Indica	2759	90.50%	0.10%	7.65%	1.74%	NA
All Japonica	1512	99.50%	0.00%	0.33%	0.13%	NA
Aus	269	99.30%	0.00%	0.74%	0.00%	NA
Indica I	595	79.00%	0.00%	18.49%	2.52%	NA
Indica II	465	94.60%	0.00%	4.73%	0.65%	NA
Indica III	913	96.80%	0.20%	1.42%	1.53%	NA
Indica Intermediate	786	89.40%	0.10%	8.40%	2.04%	NA
Temperate Japonica	767	99.90%	0.00%	0.00%	0.13%	NA
Tropical Japonica	504	99.00%	0.00%	0.79%	0.20%	NA
Japonica Intermediate	241	99.60%	0.00%	0.41%	0.00%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	96.70%	1.10%	2.22%	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
vg0726119227	C -> DEL	LOC_Os07g43630.1	N	frameshift_variant	Average:22.284; most accessible tissue: Zhenshan97 root, score: 39.742	N	N	N	N
vg0726119227	C -> T	LOC_Os07g43630.1	synonymous_variant ; p.Arg419Arg; LOW	synonymous_codon	Average:22.284; most accessible tissue: Zhenshan97 root, score: 39.742	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0726119227	7.52E-06	NA	mr1011_2	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