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Detailed information for vg0403528964:

Variant ID: vg0403528964 (JBrowse)	Variation Type: SNP
Chromosome: chr04	Position: 3528964
Reference Allele: C	Alternative Allele: A
Primary Allele: C	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

AGTGCCTGTCAACTTTACAAAGATTCCGACATCCCACAAATCTGTCCAATGAGCTGACTCCTTTAACGATGACAAATTAAGGATAATGATGATTTGGCAA[C/A]
AAGTGTGCCACTGATATGCTAATGATATCCACACATTAATGTCCCTGTTGCATTTCTTTAGAGTCGAACTAATTAAACGCCGAAAGTTATTCCATACTTT

Reverse complement sequence

AAAGTATGGAATAACTTTCGGCGTTTAATTAGTTCGACTCTAAAGAAATGCAACAGGGACATTAATGTGTGGATATCATTAGCATATCAGTGGCACACTT[G/T]
TTGCCAAATCATCATTATCCTTAATTTGTCATCGTTAAAGGAGTCAGCTCATTGGACAGATTTGTGGGATGTCGGAATCTTTGTAAAGTTGACAGGCACT

Allele Frequencies:

Populations	Population Size	Frequency of C(primary allele)	Frequency of A(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	60.00%	4.10%	3.62%	32.25%	NA
All Indica	2759	43.80%	1.50%	5.47%	49.26%	NA
All Japonica	1512	81.30%	10.00%	0.53%	8.13%	NA
Aus	269	98.10%	0.00%	1.12%	0.74%	NA
Indica I	595	31.80%	0.00%	4.20%	64.03%	NA
Indica II	465	57.60%	1.70%	3.01%	37.63%	NA
Indica III	913	38.80%	2.70%	5.91%	52.57%	NA
Indica Intermediate	786	50.50%	1.00%	7.38%	41.09%	NA
Temperate Japonica	767	78.60%	18.10%	0.13%	3.13%	NA
Tropical Japonica	504	88.10%	0.60%	0.60%	10.71%	NA
Japonica Intermediate	241	75.90%	3.70%	1.66%	18.67%	NA
VI/Aromatic	96	76.00%	1.00%	4.17%	18.75%	NA
Intermediate	90	68.90%	1.10%	5.56%	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
vg0403528964	C -> DEL	N	N	silent_mutation	Average:44.538; most accessible tissue: Minghui63 panicle, score: 76.913	N	N	N	N
vg0403528964	C -> A	LOC_Os04g06700.1	downstream_gene_variant ; 950.0bp to feature; MODIFIER	silent_mutation	Average:44.538; most accessible tissue: Minghui63 panicle, score: 76.913	N	N	N	N
vg0403528964	C -> A	LOC_Os04g06690-LOC_Os04g06700	intergenic_region ; MODIFIER	silent_mutation	Average:44.538; most accessible tissue: Minghui63 panicle, score: 76.913	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0403528964	2.32E-15	1.44E-31	Awn_length	All	YES	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
vg0403528964	NA	4.55E-14	Awn_length	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
vg0403528964	3.74E-06	3.27E-12	Heading_date	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
vg0403528964	NA	6.79E-12	Heading_date	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
vg0403528964	NA	1.14E-08	mr1549	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
vg0403528964	NA	2.60E-09	mr1757	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
vg0403528964	NA	2.66E-08	mr1549_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
vg0403528964	NA	7.54E-06	mr1723_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
vg0403528964	NA	2.72E-08	mr1757_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