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Detailed information for vg0624437748:

Variant ID: vg0624437748 (JBrowse)	Variation Type: SNP
Chromosome: chr06	Position: 24437748
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.96, C: 0.04, others allele: 0.00, population size: 222. )

Flanking Sequence (100 bp) in Reference Genome:

CAACAAACAGTATCGACACTGAATCCGGGCCGGCCACATAAAAGGAGAAACATATGCCGTCAGGCTAGAGGCTTTATTGGTGTGGTTCAGTACTTGATAA[C/T]
TGATCATAGACAGAGTTCGGGGGAGAAAAATGAACTTTATTTATTTTTCTTCAGGGTACGTACGATTATTAGTAATCAATTTATAAAACGTAGTGATACT

Reverse complement sequence

AGTATCACTACGTTTTATAAATTGATTACTAATAATCGTACGTACCCTGAAGAAAAATAAATAAAGTTCATTTTTCTCCCCCGAACTCTGTCTATGATCA[G/A]
TTATCAAGTACTGAACCACACCAATAAAGCCTCTAGCCTGACGGCATATGTTTCTCCTTTTATGTGGCCGGCCCGGATTCAGTGTCGATACTGTTTGTTG

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	68.60%	31.40%	0.04%	0.00%	NA
All Indica	2759	62.50%	37.40%	0.07%	0.00%	NA
All Japonica	1512	89.60%	10.40%	0.00%	0.00%	NA
Aus	269	5.90%	94.10%	0.00%	0.00%	NA
Indica I	595	85.00%	14.80%	0.17%	0.00%	NA
Indica II	465	74.00%	26.00%	0.00%	0.00%	NA
Indica III	913	48.40%	51.60%	0.00%	0.00%	NA
Indica Intermediate	786	55.00%	44.90%	0.13%	0.00%	NA
Temperate Japonica	767	99.50%	0.50%	0.00%	0.00%	NA
Tropical Japonica	504	71.40%	28.60%	0.00%	0.00%	NA
Japonica Intermediate	241	95.90%	4.10%	0.00%	0.00%	NA
VI/Aromatic	96	86.50%	13.50%	0.00%	0.00%	NA
Intermediate	90	71.10%	28.90%	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
vg0624437748	C -> T	LOC_Os06g40950-LOC_Os06g40960	intergenic_region ; MODIFIER	silent_mutation	Average:63.206; most accessible tissue: Minghui63 panicle, score: 82.128	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0624437748	NA	5.78E-12	Grain_width	Jap_All	Not	Breeding signatures of rice improvement revealed by a genomic variation map from a large germplasm collection, Proc Natl Acad Sci USA, 112(39): E5411-E5419, PMID:26358652
vg0624437748	NA	1.67E-06	mr1073	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
vg0624437748	NA	3.37E-06	mr1082	Jap_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
vg0624437748	NA	1.95E-07	mr1583	Jap_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
vg0624437748	7.14E-06	NA	mr1138_2	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
vg0624437748	3.62E-07	NA	mr1138_2	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
vg0624437748	NA	7.78E-07	mr1188_2	Jap_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
vg0624437748	NA	3.59E-06	mr1740_2	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
vg0624437748	NA	3.22E-07	mr1850_2	Jap_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