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Detailed information for vg0622757649:

Variant ID: vg0622757649 (JBrowse)	Variation Type: SNP
Chromosome: chr06	Position: 22757649
Reference Allele: T	Alternative Allele: C
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.99, C: 0.01, others allele: 0.00, population size: 132. )

Flanking Sequence (100 bp) in Reference Genome:

GTCCCATTAATTTACGCTGTCATAACTGTATCCTCAACCATTTGGATTTCAAACAGCGCAAGCCACCAGGATGGCCCAAATGGAGAAACAAATTGAAGCC[T/C]
TGAAAAGAGACAAGGTAGAACTGGCTGCACAAAGGGACTCGGCCTTGAAGGAGATTGAAGGTACTGCCAGCTAACAATCTGAACTTCTCTCTTTTAAATG

Reverse complement sequence

CATTTAAAAGAGAGAAGTTCAGATTGTTAGCTGGCAGTACCTTCAATCTCCTTCAAGGCCGAGTCCCTTTGTGCAGCCAGTTCTACCTTGTCTCTTTTCA[A/G]
GGCTTCAATTTGTTTCTCCATTTGGGCCATCCTGGTGGCTTGCGCTGTTTGAAATCCAAATGGTTGAGGATACAGTTATGACAGCGTAAATTAATGGGAC

Allele Frequencies:

Populations	Population Size	Frequency of T(primary allele)	Frequency of C(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	74.70%	10.50%	5.14%	9.61%	NA
All Indica	2759	74.80%	12.00%	5.65%	7.58%	NA
All Japonica	1512	81.40%	1.40%	3.51%	13.69%	NA
Aus	269	57.20%	22.30%	8.55%	11.90%	NA
Indica I	595	81.50%	7.20%	2.86%	8.40%	NA
Indica II	465	74.60%	8.80%	7.96%	8.60%	NA
Indica III	913	70.40%	17.70%	5.37%	6.46%	NA
Indica Intermediate	786	74.80%	10.80%	6.74%	7.63%	NA
Temperate Japonica	767	81.10%	0.90%	3.00%	14.99%	NA
Tropical Japonica	504	89.50%	1.40%	2.38%	6.75%	NA
Japonica Intermediate	241	65.60%	2.90%	7.47%	24.07%	NA
VI/Aromatic	96	16.70%	75.00%	8.33%	0.00%	NA
Intermediate	90	75.60%	14.40%	3.33%	6.67%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0622757649	T -> C	LOC_Os06g38410.1	synonymous_variant ; p.Leu577Leu; LOW	synonymous_codon	Average:12.577; most accessible tissue: Zhenshan97 root, score: 20.427	N	N	N	N
vg0622757649	T -> DEL	LOC_Os06g38410.1	N	frameshift_variant	Average:12.577; most accessible tissue: Zhenshan97 root, score: 20.427	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0622757649	3.12E-06	3.12E-06	mr1348	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