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Detailed information for vg0507146035:

Variant ID: vg0507146035 (JBrowse)	Variation Type: SNP
Chromosome: chr05	Position: 7146035
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.01, others allele: 0.00, population size: 295. )

Flanking Sequence (100 bp) in Reference Genome:

AGTAGGACTCCGATAATCTCCAGCCCGTGAGGATATTTTCCATGCTATCTCGTATATTTCCTTATCGCATACAGAAACATATCGTAGGATACGGGTATGC[C/T]
AATCTTGTATATTTGGTAAATCGTAGGATAGTAGGTATGCCTTATCCGTAACCCTGACACATCTGACGTTTCTTTGAGACAAGCAACAAGATTCCAGAAG

Reverse complement sequence

CTTCTGGAATCTTGTTGCTTGTCTCAAAGAAACGTCAGATGTGTCAGGGTTACGGATAAGGCATACCTACTATCCTACGATTTACCAAATATACAAGATT[G/A]
GCATACCCGTATCCTACGATATGTTTCTGTATGCGATAAGGAAATATACGAGATAGCATGGAAAATATCCTCACGGGCTGGAGATTATCGGAGTCCTACT

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	97.80%	1.70%	0.55%	0.00%	NA
All Indica	2759	100.00%	0.00%	0.00%	0.00%	NA
All Japonica	1512	93.20%	5.10%	1.72%	0.00%	NA
Aus	269	100.00%	0.00%	0.00%	0.00%	NA
Indica I	595	100.00%	0.00%	0.00%	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	99.90%	0.10%	0.00%	0.00%	NA
Temperate Japonica	767	90.00%	7.20%	2.87%	0.00%	NA
Tropical Japonica	504	99.40%	0.60%	0.00%	0.00%	NA
Japonica Intermediate	241	90.50%	7.90%	1.66%	0.00%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	98.90%	1.10%	0.00%	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
vg0507146035	C -> T	LOC_Os05g12420.1	downstream_gene_variant ; 3694.0bp to feature; MODIFIER	silent_mutation	Average:64.595; most accessible tissue: Zhenshan97 flower, score: 82.111	N	N	N	N
vg0507146035	C -> T	LOC_Os05g12440.1	downstream_gene_variant ; 3627.0bp to feature; MODIFIER	silent_mutation	Average:64.595; most accessible tissue: Zhenshan97 flower, score: 82.111	N	N	N	N
vg0507146035	C -> T	LOC_Os05g12430.1	intron_variant ; MODIFIER	silent_mutation	Average:64.595; most accessible tissue: Zhenshan97 flower, score: 82.111	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0507146035	3.62E-06	3.62E-06	mr1456	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