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Detailed information for vg0509011910:

Variant ID: vg0509011910 (JBrowse)	Variation Type: SNP
Chromosome: chr05	Position: 9011910
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: 291. )

Flanking Sequence (100 bp) in Reference Genome:

ACCCAAACTCCATAGTTCACATCGCCAATTTCATTCATGCCTGCGAAGCCTTTTTAGGTATTAGGCCGTATTTCGCCTTGTTCCGCCGCATCTTCTTCCT[C/T]
AAACCTCAGCCAAACAAGAGCAAACCATGTGTTGTTGGGGGGGCTGGCTTCCAACTCAGGGGAACCTTAAGCCAAAAATACTTCTCTATGCCCTTCAAAA

Reverse complement sequence

TTTTGAAGGGCATAGAGAAGTATTTTTGGCTTAAGGTTCCCCTGAGTTGGAAGCCAGCCCCCCCAACAACACATGGTTTGCTCTTGTTTGGCTGAGGTTT[G/A]
AGGAAGAAGATGCGGCGGAACAAGGCGAAATACGGCCTAATACCTAAAAAGGCTTCGCAGGCATGAATGAAATTGGCGATGTGAACTATGGAGTTTGGGT

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	97.10%	2.80%	0.17%	0.00%	NA
All Indica	2759	95.00%	4.70%	0.29%	0.00%	NA
All Japonica	1512	100.00%	0.00%	0.00%	0.00%	NA
Aus	269	100.00%	0.00%	0.00%	0.00%	NA
Indica I	595	92.10%	7.40%	0.50%	0.00%	NA
Indica II	465	93.50%	6.20%	0.22%	0.00%	NA
Indica III	913	97.60%	2.30%	0.11%	0.00%	NA
Indica Intermediate	786	95.00%	4.60%	0.38%	0.00%	NA
Temperate Japonica	767	100.00%	0.00%	0.00%	0.00%	NA
Tropical Japonica	504	100.00%	0.00%	0.00%	0.00%	NA
Japonica Intermediate	241	100.00%	0.00%	0.00%	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
vg0509011910	C -> T	LOC_Os05g15950.1	downstream_gene_variant ; 2932.0bp to feature; MODIFIER	silent_mutation	Average:39.853; most accessible tissue: Minghui63 flag leaf, score: 56.489	N	N	N	N
vg0509011910	C -> T	LOC_Os05g15970.1	downstream_gene_variant ; 2880.0bp to feature; MODIFIER	silent_mutation	Average:39.853; most accessible tissue: Minghui63 flag leaf, score: 56.489	N	N	N	N
vg0509011910	C -> T	LOC_Os05g15960.1	intron_variant ; MODIFIER	silent_mutation	Average:39.853; most accessible tissue: Minghui63 flag leaf, score: 56.489	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0509011910	2.39E-06	2.15E-06	mr1256	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
vg0509011910	NA	1.12E-09	mr1023_2	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