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Detailed information for vg1007488823:

Variant ID: vg1007488823 (JBrowse)	Variation Type: SNP
Chromosome: chr10	Position: 7488823
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: 32. )

Flanking Sequence (100 bp) in Reference Genome:

CAGCAACGAAAGAAGTCGAGGAAGAAACCAAAGCACTAGACTTAGGATCAACTTTACGAGAAAGAATATTCATCTCATATGTTTTGAGTTTTGTGTAAAG[C/T]
GAATCCAAAGTCAAAGTAGACATATCAACAGACTCCTGAATTGATGTAACTTTCATCTCCCAAATAGACATGTCAAGACCACTCAAAAAGTAATGAGAAA

Reverse complement sequence

TTTCTCATTACTTTTTGAGTGGTCTTGACATGTCTATTTGGGAGATGAAAGTTACATCAATTCAGGAGTCTGTTGATATGTCTACTTTGACTTTGGATTC[G/A]
CTTTACACAAAACTCAAAACATATGAGATGAATATTCTTTCTCGTAAAGTTGATCCTAAGTCTAGTGCTTTGGTTTCTTCCTCGACTTCTTTCGTTGCTG

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	57.20%	6.60%	8.29%	27.89%	NA
All Indica	2759	53.80%	9.30%	11.45%	25.44%	NA
All Japonica	1512	71.80%	1.30%	3.84%	23.08%	NA
Aus	269	16.40%	10.80%	2.23%	70.63%	NA
Indica I	595	26.70%	4.50%	19.66%	49.08%	NA
Indica II	465	71.60%	3.70%	5.38%	19.35%	NA
Indica III	913	59.80%	15.00%	11.17%	14.02%	NA
Indica Intermediate	786	56.70%	9.70%	9.16%	24.43%	NA
Temperate Japonica	767	61.00%	1.40%	5.87%	31.68%	NA
Tropical Japonica	504	85.90%	1.00%	1.19%	11.90%	NA
Japonica Intermediate	241	76.80%	1.20%	2.90%	19.09%	NA
VI/Aromatic	96	31.20%	4.20%	9.38%	55.21%	NA
Intermediate	90	67.80%	2.20%	3.33%	26.67%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1007488823	C -> T	LOC_Os10g13770.1	synonymous_variant ; p.Ser174Ser; LOW	synonymous_codon	Average:9.357; most accessible tissue: Callus, score: 39.671	N	N	N	N
vg1007488823	C -> DEL	LOC_Os10g13770.1	N	frameshift_variant	Average:9.357; most accessible tissue: Callus, score: 39.671	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1007488823	NA	1.52E-07	mr1551	Jap_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