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Detailed information for vg0410045473:

Variant ID: vg0410045473 (JBrowse)	Variation Type: SNP
Chromosome: chr04	Position: 10045473
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: 313. )

Flanking Sequence (100 bp) in Reference Genome:

AAGAAAAAGGATCCAGAAGGATAAGACGTTTGGCTTATACTCCAGTTTAGCTGCCTGTGGGAGTGGAGCTGAAGCCATCGCTAGACCGTTAATTCCGCTG[C/T]
TGTTTTCTTTTCTTTTGTAAGTATGTAATGATGTTATTATGATGGATTTGTATATTAAATTATCAGTTTGTGTACCTCGGCTAATTCCTGGACGAGGGTT

Reverse complement sequence

AACCCTCGTCCAGGAATTAGCCGAGGTACACAAACTGATAATTTAATATACAAATCCATCATAATAACATCATTACATACTTACAAAAGAAAAGAAAACA[G/A]
CAGCGGAATTAACGGTCTAGCGATGGCTTCAGCTCCACTCCCACAGGCAGCTAAACTGGAGTATAAGCCAAACGTCTTATCCTTCTGGATCCTTTTTCTT

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	85.90%	11.10%	0.78%	2.22%	NA
All Indica	2759	99.50%	0.30%	0.04%	0.14%	NA
All Japonica	1512	63.20%	28.40%	1.92%	6.48%	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	98.70%	0.60%	0.22%	0.43%	NA
Indica III	913	99.80%	0.10%	0.00%	0.11%	NA
Indica Intermediate	786	99.40%	0.50%	0.00%	0.13%	NA
Temperate Japonica	767	96.60%	2.70%	0.26%	0.39%	NA
Tropical Japonica	504	8.30%	69.40%	5.36%	16.87%	NA
Japonica Intermediate	241	71.80%	24.10%	0.00%	4.15%	NA
VI/Aromatic	96	19.80%	72.90%	6.25%	1.04%	NA
Intermediate	90	76.70%	20.00%	1.11%	2.22%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0410045473	C -> DEL	N	N	silent_mutation	Average:42.049; most accessible tissue: Minghui63 flag leaf, score: 64.284	N	N	N	N
vg0410045473	C -> T	LOC_Os04g18170.1	intron_variant ; MODIFIER	silent_mutation	Average:42.049; most accessible tissue: Minghui63 flag leaf, score: 64.284	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0410045473	1.36E-06	NA	Awn_length	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
vg0410045473	NA	9.26E-08	mr1220	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
vg0410045473	NA	3.40E-06	mr1220	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
vg0410045473	NA	4.22E-07	mr1229	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
vg0410045473	NA	4.84E-06	mr1328	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
vg0410045473	NA	1.16E-06	mr1338	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
vg0410045473	NA	8.39E-06	mr1378	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
vg0410045473	NA	8.26E-07	mr1425	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
vg0410045473	NA	4.37E-06	mr1425	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
vg0410045473	NA	3.14E-06	mr1446	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
vg0410045473	5.45E-06	NA	mr1526	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
vg0410045473	NA	4.79E-07	mr1642	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
vg0410045473	NA	8.55E-07	mr1739	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
vg0410045473	NA	9.83E-20	mr1301_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