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Detailed information for vg0613263498:

Variant ID: vg0613263498 (JBrowse)	Variation Type: SNP
Chromosome: chr06	Position: 13263498
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.99, others allele: 0.00, population size: 232. )

Flanking Sequence (100 bp) in Reference Genome:

GGCTCGGTACTTGCAAGGGGTGCGCCGTTATCATAATCGCAATGTTCGATCACGAGCTTTTTTAGTCGGCGACCTGGTTCTGAGAAAAATTCAAACTACA[C/T]
AGGATCGGCACAAGTTATCTCCCTTATGGGAAGGACCATTCATAATTTCCAAAGTCACTCGGCCAGGTTCTTACCGACTCAAGCGTGAAGACGGTACTCC

Reverse complement sequence

GGAGTACCGTCTTCACGCTTGAGTCGGTAAGAACCTGGCCGAGTGACTTTGGAAATTATGAATGGTCCTTCCCATAAGGGAGATAACTTGTGCCGATCCT[G/A]
TGTAGTTTGAATTTTTCTCAGAACCAGGTCGCCGACTAAAAAAGCTCGTGATCGAACATTGCGATTATGATAACGGCGCACCCCTTGCAAGTACCGAGCC

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	50.00%	49.70%	0.21%	0.13%	NA
All Indica	2759	21.20%	78.40%	0.25%	0.18%	NA
All Japonica	1512	97.60%	2.30%	0.13%	0.00%	NA
Aus	269	61.30%	38.30%	0.37%	0.00%	NA
Indica I	595	19.30%	80.20%	0.34%	0.17%	NA
Indica II	465	9.90%	89.70%	0.22%	0.22%	NA
Indica III	913	28.50%	71.10%	0.22%	0.22%	NA
Indica Intermediate	786	20.90%	78.80%	0.25%	0.13%	NA
Temperate Japonica	767	96.50%	3.50%	0.00%	0.00%	NA
Tropical Japonica	504	98.80%	1.00%	0.20%	0.00%	NA
Japonica Intermediate	241	98.30%	1.20%	0.41%	0.00%	NA
VI/Aromatic	96	85.40%	14.60%	0.00%	0.00%	NA
Intermediate	90	60.00%	38.90%	0.00%	1.11%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0613263498	C -> T	LOC_Os06g22770.1	downstream_gene_variant ; 1222.0bp to feature; MODIFIER	silent_mutation	Average:35.469; most accessible tissue: Zhenshan97 flag leaf, score: 59.429	N	N	N	N
vg0613263498	C -> T	LOC_Os06g22790.1	downstream_gene_variant ; 476.0bp to feature; MODIFIER	silent_mutation	Average:35.469; most accessible tissue: Zhenshan97 flag leaf, score: 59.429	N	N	N	N
vg0613263498	C -> T	LOC_Os06g22780.1	intron_variant ; MODIFIER	silent_mutation	Average:35.469; most accessible tissue: Zhenshan97 flag leaf, score: 59.429	N	N	N	N
vg0613263498	C -> DEL	N	N	silent_mutation	Average:35.469; most accessible tissue: Zhenshan97 flag leaf, score: 59.429	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0613263498	3.86E-06	NA	mr1141_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