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Detailed information for vg0909595977:

Variant ID: vg0909595977 (JBrowse)	Variation Type: SNP
Chromosome: chr09	Position: 9595977
Reference Allele: C	Alternative Allele: A
Primary Allele: C	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

TTCATATCTAATTCATATGAACTCCGAATTGAGCCATTCAACTTGCAAAATTCATCTAAAATTGAGCTCTACATGTTTGTTTAGTTTTTATGTACTTTTT[C/A]
GTTGGTTTTTATTAGAGTTTTTCCTCGTTTTGCGTGCCAGTGTGTAGAATCCGTCGTTTTGAAAGTTCGCGGTCGCAAGGATAAGAGTTCGGAAGATTGT

Reverse complement sequence

ACAATCTTCCGAACTCTTATCCTTGCGACCGCGAACTTTCAAAACGACGGATTCTACACACTGGCACGCAAAACGAGGAAAAACTCTAATAAAAACCAAC[G/T]
AAAAAGTACATAAAAACTAAACAAACATGTAGAGCTCAATTTTAGATGAATTTTGCAAGTTGAATGGCTCAATTCGGAGTTCATATGAATTAGATATGAA

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	80.80%	2.80%	1.27%	15.17%	NA
All Indica	2759	83.60%	0.10%	1.01%	15.33%	NA
All Japonica	1512	77.00%	8.40%	0.60%	14.02%	NA
Aus	269	79.60%	0.00%	0.37%	20.07%	NA
Indica I	595	85.20%	0.00%	0.17%	14.62%	NA
Indica II	465	83.20%	0.00%	0.22%	16.56%	NA
Indica III	913	82.00%	0.00%	2.52%	15.44%	NA
Indica Intermediate	786	84.40%	0.30%	0.38%	15.01%	NA
Temperate Japonica	767	77.60%	6.80%	0.78%	14.86%	NA
Tropical Japonica	504	76.80%	11.50%	0.20%	11.51%	NA
Japonica Intermediate	241	75.50%	7.10%	0.83%	16.60%	NA
VI/Aromatic	96	59.40%	0.00%	20.83%	19.79%	NA
Intermediate	90	86.70%	1.10%	2.22%	10.00%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0909595977	C -> DEL	N	N	silent_mutation	Average:24.678; most accessible tissue: Zhenshan97 panicle, score: 52.263	N	N	N	N
vg0909595977	C -> A	LOC_Os09g15720.1	upstream_gene_variant ; 874.0bp to feature; MODIFIER	silent_mutation	Average:24.678; most accessible tissue: Zhenshan97 panicle, score: 52.263	N	N	N	N
vg0909595977	C -> A	LOC_Os09g15710.1	downstream_gene_variant ; 4070.0bp to feature; MODIFIER	silent_mutation	Average:24.678; most accessible tissue: Zhenshan97 panicle, score: 52.263	N	N	N	N
vg0909595977	C -> A	LOC_Os09g15720-LOC_Os09g15740	intergenic_region ; MODIFIER	silent_mutation	Average:24.678; most accessible tissue: Zhenshan97 panicle, score: 52.263	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0909595977	9.42E-09	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
vg0909595977	NA	3.62E-08	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
vg0909595977	2.19E-08	NA	mr1549_2	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