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Detailed information for vg0810032310:

Variant ID: vg0810032310 (JBrowse)	Variation Type: SNP
Chromosome: chr08	Position: 10032310
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.93, T: 0.06, others allele: 0.00, population size: 107. )

Flanking Sequence (100 bp) in Reference Genome:

GCTAGGAAAATGGACTTATAGATGGATGAGAATTAAAGAGAAGATATTGAAGATGCGGTATGAAGTGACTACCTATGTCAAGATGGTGAAGCGCAAGCGA[C/T]
ACTCAACTGCGATGGACCATGCGGTGGTGAAGGGCAAGTGAGGGGCTTGGCGCCGACGAACCGAAACCGGTGGTGAAGGGCGAGTGAGGATTGTGTCGTG

Reverse complement sequence

CACGACACAATCCTCACTCGCCCTTCACCACCGGTTTCGGTTCGTCGGCGCCAAGCCCCTCACTTGCCCTTCACCACCGCATGGTCCATCGCAGTTGAGT[G/A]
TCGCTTGCGCTTCACCATCTTGACATAGGTAGTCACTTCATACCGCATCTTCAATATCTTCTCTTTAATTCTCATCCATCTATAAGTCCATTTTCCTAGC

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	45.70%	28.30%	1.14%	24.78%	NA
All Indica	2759	34.60%	46.50%	1.45%	17.47%	NA
All Japonica	1512	58.60%	1.90%	0.73%	38.82%	NA
Aus	269	97.80%	0.70%	0.00%	1.49%	NA
Indica I	595	49.20%	46.20%	0.84%	3.70%	NA
Indica II	465	38.50%	40.60%	1.72%	19.14%	NA
Indica III	913	25.70%	45.90%	1.31%	27.05%	NA
Indica Intermediate	786	31.40%	50.90%	1.91%	15.78%	NA
Temperate Japonica	767	89.60%	1.60%	0.26%	8.60%	NA
Tropical Japonica	504	18.50%	2.20%	1.79%	77.58%	NA
Japonica Intermediate	241	44.00%	2.10%	0.00%	53.94%	NA
VI/Aromatic	96	12.50%	6.20%	2.08%	79.17%	NA
Intermediate	90	52.20%	22.20%	1.11%	24.44%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0810032310	C -> T	LOC_Os08g16420.1	upstream_gene_variant ; 4669.0bp to feature; MODIFIER	silent_mutation	Average:39.776; most accessible tissue: Minghui63 panicle, score: 53.77	N	N	N	N
vg0810032310	C -> T	LOC_Os08g16410.1	downstream_gene_variant ; 3802.0bp to feature; MODIFIER	silent_mutation	Average:39.776; most accessible tissue: Minghui63 panicle, score: 53.77	N	N	N	N
vg0810032310	C -> T	LOC_Os08g16400-LOC_Os08g16410	intergenic_region ; MODIFIER	silent_mutation	Average:39.776; most accessible tissue: Minghui63 panicle, score: 53.77	N	N	N	N
vg0810032310	C -> DEL	N	N	silent_mutation	Average:39.776; most accessible tissue: Minghui63 panicle, score: 53.77	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0810032310	4.93E-06	1.69E-07	mr1368	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