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Detailed information for vg0618200340:

Variant ID: vg0618200340 (JBrowse)	Variation Type: SNP
Chromosome: chr06	Position: 18200340
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: 263. )

Flanking Sequence (100 bp) in Reference Genome:

CAGTGCATCTGTATACTTCCTTCAACTTGGCCTGTACTGAGAAAAAAATCGGTGTGTATCGTTCATCAGAAAAAAAATATACCAAGGCCGTGTTTAGATT[C/T]
AAACTTTTTTCTTCAAACTTTCAACTTTTCCGTCACATCAAATGTTTGGACATATGCATGGAGCATTAAATGTGGACGAAAAAAAATAATTACACAGTTT

Reverse complement sequence

AAACTGTGTAATTATTTTTTTTCGTCCACATTTAATGCTCCATGCATATGTCCAAACATTTGATGTGACGGAAAAGTTGAAAGTTTGAAGAAAAAAGTTT[G/A]
AATCTAAACACGGCCTTGGTATATTTTTTTTCTGATGAACGATACACACCGATTTTTTTCTCAGTACAGGCCAAGTTGAAGGAAGTATACAGATGCACTG

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	89.30%	10.30%	0.36%	0.00%	NA
All Indica	2759	99.40%	0.40%	0.14%	0.00%	NA
All Japonica	1512	68.10%	31.20%	0.79%	0.00%	NA
Aus	269	100.00%	0.00%	0.00%	0.00%	NA
Indica I	595	98.00%	1.70%	0.34%	0.00%	NA
Indica II	465	100.00%	0.00%	0.00%	0.00%	NA
Indica III	913	100.00%	0.00%	0.00%	0.00%	NA
Indica Intermediate	786	99.50%	0.30%	0.25%	0.00%	NA
Temperate Japonica	767	58.80%	39.80%	1.43%	0.00%	NA
Tropical Japonica	504	93.10%	6.90%	0.00%	0.00%	NA
Japonica Intermediate	241	45.20%	54.40%	0.41%	0.00%	NA
VI/Aromatic	96	99.00%	1.00%	0.00%	0.00%	NA
Intermediate	90	94.40%	4.40%	1.11%	0.00%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0618200340	C -> T	LOC_Os06g31290.1	upstream_gene_variant ; 4464.0bp to feature; MODIFIER	silent_mutation	Average:47.818; most accessible tissue: Minghui63 flower, score: 64.685	N	N	N	N
vg0618200340	C -> T	LOC_Os06g31280.1	downstream_gene_variant ; 1833.0bp to feature; MODIFIER	silent_mutation	Average:47.818; most accessible tissue: Minghui63 flower, score: 64.685	N	N	N	N
vg0618200340	C -> T	LOC_Os06g31270-LOC_Os06g31280	intergenic_region ; MODIFIER	silent_mutation	Average:47.818; most accessible tissue: Minghui63 flower, score: 64.685	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0618200340	4.68E-06	4.68E-06	mr1197	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