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Detailed information for vg1014305507:

Variant ID: vg1014305507 (JBrowse)	Variation Type: SNP
Chromosome: chr10	Position: 14305507
Reference Allele: T	Alternative Allele: C
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.97, T: 0.03, others allele: 0.00, population size: 109. )

Flanking Sequence (100 bp) in Reference Genome:

TGTTGTTGACCATATTTCCATTTGAAATCTTTTACTATCCGAAAATGTATTATGACTAATAAAATGAATTATTACACAGCTGCTATATATTTTGCACTCA[T/C]
AACAAATGAAAGATGGAAAATGAGTCATCGGTGATGGGCCTTAGTTTACGGCCGATAGAGATTAATCTATCTCAATCGGGCTTTGCCGTAGGGCCCGTCA

Reverse complement sequence

TGACGGGCCCTACGGCAAAGCCCGATTGAGATAGATTAATCTCTATCGGCCGTAAACTAAGGCCCATCACCGATGACTCATTTTCCATCTTTCATTTGTT[A/G]
TGAGTGCAAAATATATAGCAGCTGTGTAATAATTCATTTTATTAGTCATAATACATTTTCGGATAGTAAAAGATTTCAAATGGAAATATGGTCAACAACA

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	44.40%	13.10%	19.81%	22.64%	NA
All Indica	2759	28.70%	1.80%	31.79%	37.66%	NA
All Japonica	1512	67.90%	31.50%	0.13%	0.53%	NA
Aus	269	80.30%	0.70%	16.36%	2.60%	NA
Indica I	595	29.60%	1.00%	28.07%	41.34%	NA
Indica II	465	17.80%	2.20%	31.40%	48.60%	NA
Indica III	913	34.40%	1.50%	34.83%	29.24%	NA
Indica Intermediate	786	27.90%	2.70%	31.30%	38.17%	NA
Temperate Japonica	767	46.00%	53.70%	0.13%	0.13%	NA
Tropical Japonica	504	94.80%	4.20%	0.20%	0.79%	NA
Japonica Intermediate	241	80.90%	17.80%	0.00%	1.24%	NA
VI/Aromatic	96	27.10%	72.90%	0.00%	0.00%	NA
Intermediate	90	43.30%	24.40%	14.44%	17.78%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1014305507	T -> C	LOC_Os10g27150.1	upstream_gene_variant ; 2163.0bp to feature; MODIFIER	silent_mutation	Average:13.718; most accessible tissue: Minghui63 panicle, score: 20.733	N	N	N	N
vg1014305507	T -> C	LOC_Os10g27140.1	downstream_gene_variant ; 408.0bp to feature; MODIFIER	silent_mutation	Average:13.718; most accessible tissue: Minghui63 panicle, score: 20.733	N	N	N	N
vg1014305507	T -> C	LOC_Os10g27140-LOC_Os10g27150	intergenic_region ; MODIFIER	silent_mutation	Average:13.718; most accessible tissue: Minghui63 panicle, score: 20.733	N	N	N	N
vg1014305507	T -> DEL	N	N	silent_mutation	Average:13.718; most accessible tissue: Minghui63 panicle, score: 20.733	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1014305507	1.70E-06	1.70E-06	mr1609	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