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Detailed information for vg0610609943:

Variant ID: vg0610609943 (JBrowse)	Variation Type: SNP
Chromosome: chr06	Position: 10609943
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, T: 0.01, others allele: 0.00, population size: 111. )

Flanking Sequence (100 bp) in Reference Genome:

TCGGTAGGCGGATCCAGCCGCTCCAGGCTCGGGCCCACCCGGCATATAACTATTCCGGGCCAGATGACGCGACCCGGGTTTCTCCTCGGGGTATCCTTCT[C/T]
GTATTCACTTTGATACATTTGTATTCACGTTCCATTTGACTTATCAAGAATTGATTCTTTCTTGACAGGTCTGAGCAGTGAAGTCATGGAGCGGTGCGCT

Reverse complement sequence

AGCGCACCGCTCCATGACTTCACTGCTCAGACCTGTCAAGAAAGAATCAATTCTTGATAAGTCAAATGGAACGTGAATACAAATGTATCAAAGTGAATAC[G/A]
AGAAGGATACCCCGAGGAGAAACCCGGGTCGCGTCATCTGGCCCGGAATAGTTATATGCCGGGTGGGCCCGAGCCTGGAGCGGCTGGATCCGCCTACCGA

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	45.70%	4.90%	7.38%	42.07%	NA
All Indica	2759	20.60%	8.20%	12.07%	59.22%	NA
All Japonica	1512	82.30%	0.10%	0.20%	17.39%	NA
Aus	269	83.30%	0.70%	1.86%	14.13%	NA
Indica I	595	15.00%	2.70%	12.44%	69.92%	NA
Indica II	465	6.20%	17.60%	16.34%	59.78%	NA
Indica III	913	24.90%	7.70%	11.83%	55.64%	NA
Indica Intermediate	786	28.20%	7.30%	9.54%	54.96%	NA
Temperate Japonica	767	87.70%	0.00%	0.26%	11.99%	NA
Tropical Japonica	504	70.60%	0.20%	0.20%	28.97%	NA
Japonica Intermediate	241	89.60%	0.00%	0.00%	10.37%	NA
VI/Aromatic	96	86.50%	1.00%	2.08%	10.42%	NA
Intermediate	90	43.30%	2.20%	6.67%	47.78%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0610609943	C -> T	LOC_Os06g18720.1	downstream_gene_variant ; 3496.0bp to feature; MODIFIER	silent_mutation	Average:13.49; most accessible tissue: Callus, score: 55.63	N	N	N	N
vg0610609943	C -> T	LOC_Os06g18710.1	intron_variant ; MODIFIER	silent_mutation	Average:13.49; most accessible tissue: Callus, score: 55.63	N	N	N	N
vg0610609943	C -> DEL	N	N	silent_mutation	Average:13.49; most accessible tissue: Callus, score: 55.63	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0610609943	6.79E-07	NA	mr1200	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
vg0610609943	3.81E-07	NA	mr1068_2	All	Not	Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0610609943	4.25E-06	NA	mr1078_2	All	Not	Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0610609943	3.59E-06	NA	mr1087_2	All	Not	Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0610609943	4.02E-08	NA	mr1090_2	All	Not	Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0610609943	1.67E-07	NA	mr1200_2	All	Not	Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0610609943	4.74E-07	NA	mr1211_2	All	Not	Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251