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Detailed information for vg0622509231:

Variant ID: vg0622509231 (JBrowse)	Variation Type: SNP
Chromosome: chr06	Position: 22509231
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: 99. )

Flanking Sequence (100 bp) in Reference Genome:

ATATATATATATATATGCTAAGTTCAATAATAGTTTAATTATCTCGTTCATACACATTTCGCTCGCGTTCGTTCTCACACTTTTAGTTCAAGTGCATTCA[C/T]
GTTCGTTAACGTTTCAATCACGTTCGTTCGCGTTTCATTCACGTTCGTTCGAGTTCGTTCACTAACACTCACGTTTGTTCACGTTTCAGTCACGTTCGTT

Reverse complement sequence

AACGAACGTGACTGAAACGTGAACAAACGTGAGTGTTAGTGAACGAACTCGAACGAACGTGAATGAAACGCGAACGAACGTGATTGAAACGTTAACGAAC[G/A]
TGAATGCACTTGAACTAAAAGTGTGAGAACGAACGCGAGCGAAATGTGTATGAACGAGATAATTAAACTATTATTGAACTTAGCATATATATATATATAT

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	70.00%	2.30%	23.47%	4.25%	NA
All Indica	2759	68.00%	3.80%	27.36%	0.76%	NA
All Japonica	1512	68.30%	0.00%	20.90%	10.85%	NA
Aus	269	92.90%	0.00%	5.95%	1.12%	NA
Indica I	595	85.70%	1.80%	12.10%	0.34%	NA
Indica II	465	78.50%	4.70%	15.27%	1.51%	NA
Indica III	913	48.60%	3.90%	47.32%	0.11%	NA
Indica Intermediate	786	71.00%	4.70%	22.90%	1.40%	NA
Temperate Japonica	767	82.50%	0.00%	10.17%	7.30%	NA
Tropical Japonica	504	48.40%	0.00%	33.93%	17.66%	NA
Japonica Intermediate	241	64.30%	0.00%	27.80%	7.88%	NA
VI/Aromatic	96	89.60%	0.00%	7.29%	3.12%	NA
Intermediate	90	71.10%	1.10%	16.67%	11.11%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0622509231	C -> T	LOC_Os06g38062.1	upstream_gene_variant ; 889.0bp to feature; MODIFIER	silent_mutation	Average:15.699; most accessible tissue: Callus, score: 30.822	N	N	N	N
vg0622509231	C -> T	LOC_Os06g38070.1	downstream_gene_variant ; 1482.0bp to feature; MODIFIER	silent_mutation	Average:15.699; most accessible tissue: Callus, score: 30.822	N	N	N	N
vg0622509231	C -> T	LOC_Os06g38062-LOC_Os06g38070	intergenic_region ; MODIFIER	silent_mutation	Average:15.699; most accessible tissue: Callus, score: 30.822	N	N	N	N
vg0622509231	C -> DEL	N	N	silent_mutation	Average:15.699; most accessible tissue: Callus, score: 30.822	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0622509231	NA	1.35E-08	mr1037	Ind_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
vg0622509231	NA	3.22E-06	mr1066	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
vg0622509231	NA	3.11E-07	mr1066	Ind_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
vg0622509231	3.13E-06	7.95E-07	mr1265	Ind_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
vg0622509231	3.42E-06	2.34E-07	mr1528	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