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Detailed information for vg1009327133:

Variant ID: vg1009327133 (JBrowse)	Variation Type: SNP
Chromosome: chr10	Position: 9327133
Reference Allele: T	Alternative Allele: C
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.94, T: 0.07, others allele: 0.00, population size: 108. )

Flanking Sequence (100 bp) in Reference Genome:

TGGATGGGTCAAAAATTGGCTGTGACCACGTCATGGCAGCTTGGATTGGTGCTTGGTTTGTTCCGAAGCCTGGAGTTGGAGCTTGCTGCCGAACGGTTGG[T/C]
GCCTGGACAGCGTTGACGAAGTCGAACTGCGGTCCTTGATTCCACAGCGAAACTCCCAGGCCCGGCTGAATCGGTGGCAACCAATTAGGCGCACCTTGAC

Reverse complement sequence

GTCAAGGTGCGCCTAATTGGTTGCCACCGATTCAGCCGGGCCTGGGAGTTTCGCTGTGGAATCAAGGACCGCAGTTCGACTTCGTCAACGCTGTCCAGGC[A/G]
CCAACCGTTCGGCAGCAAGCTCCAACTCCAGGCTTCGGAACAAACCAAGCACCAATCCAAGCTGCCATGACGTGGTCACAGCCAATTTTTGACCCATCCA

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	64.50%	23.00%	11.93%	0.55%	NA
All Indica	2759	76.80%	9.20%	13.01%	0.91%	NA
All Japonica	1512	46.80%	40.90%	12.30%	0.00%	NA
Aus	269	55.80%	39.40%	4.83%	0.00%	NA
Indica I	595	81.80%	4.20%	13.78%	0.17%	NA
Indica II	465	77.40%	5.20%	15.91%	1.51%	NA
Indica III	913	77.20%	13.50%	8.54%	0.77%	NA
Indica Intermediate	786	72.30%	10.60%	15.90%	1.27%	NA
Temperate Japonica	767	58.80%	25.80%	15.38%	0.00%	NA
Tropical Japonica	504	24.60%	65.30%	10.12%	0.00%	NA
Japonica Intermediate	241	55.20%	37.80%	7.05%	0.00%	NA
VI/Aromatic	96	19.80%	78.10%	2.08%	0.00%	NA
Intermediate	90	56.70%	37.80%	4.44%	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
vg1009327133	T -> C	LOC_Os10g18360.1	synonymous_variant ; p.Ala198Ala; LOW	synonymous_codon	Average:37.994; most accessible tissue: Zhenshan97 flag leaf, score: 57.42	N	N	N	N
vg1009327133	T -> DEL	LOC_Os10g18360.1	N	frameshift_variant	Average:37.994; most accessible tissue: Zhenshan97 flag leaf, score: 57.42	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1009327133	3.00E-06	3.00E-06	mr1019	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