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Detailed information for vg0712961657:

Variant ID: vg0712961657 (JBrowse)	Variation Type: SNP
Chromosome: chr07	Position: 12961657
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

GCCTAGAGAGGGGTGAATAGGCGTTCCTAAAAATTATCACAACTTAATAGCATATTGGAATGATGAGAACTTTCGATTCAAATCGGAACTTCCGGTATGG[G/A]
ATTCGAAGTTCCGGTCTCAACCGAAAAGTTAGGCGGACAACGGAATAAAACACTAGCTATGAACTTGTACCTCAAACAAACAAAATGTATATGAATCAAA

Reverse complement sequence

TTTGATTCATATACATTTTGTTTGTTTGAGGTACAAGTTCATAGCTAGTGTTTTATTCCGTTGTCCGCCTAACTTTTCGGTTGAGACCGGAACTTCGAAT[C/T]
CCATACCGGAAGTTCCGATTTGAATCGAAAGTTCTCATCATTCCAATATGCTATTAAGTTGTGATAATTTTTAGGAACGCCTATTCACCCCTCTCTAGGC

Allele Frequencies:

Populations	Population Size	Frequency of G(primary allele)	Frequency of A(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	40.40%	7.40%	1.84%	50.28%	NA
All Indica	2759	19.80%	4.50%	1.05%	74.66%	NA
All Japonica	1512	81.50%	10.10%	3.24%	5.16%	NA
Aus	269	27.10%	15.20%	1.49%	56.13%	NA
Indica I	595	25.50%	0.00%	1.18%	73.28%	NA
Indica II	465	32.00%	2.80%	0.86%	64.30%	NA
Indica III	913	6.70%	6.50%	0.88%	85.98%	NA
Indica Intermediate	786	23.30%	6.70%	1.27%	68.70%	NA
Temperate Japonica	767	78.10%	10.20%	5.74%	6.00%	NA
Tropical Japonica	504	86.70%	12.10%	0.20%	0.99%	NA
Japonica Intermediate	241	81.70%	5.40%	1.66%	11.20%	NA
VI/Aromatic	96	8.30%	31.20%	5.21%	55.21%	NA
Intermediate	90	57.80%	4.40%	0.00%	37.78%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0712961657	G -> DEL	N	N	silent_mutation	Average:10.967; most accessible tissue: Callus, score: 22.412	N	N	N	N
vg0712961657	G -> A	LOC_Os07g22970.1	downstream_gene_variant ; 3232.0bp to feature; MODIFIER	silent_mutation	Average:10.967; most accessible tissue: Callus, score: 22.412	N	N	N	N
vg0712961657	G -> A	LOC_Os07g22970-LOC_Os07g22980	intergenic_region ; MODIFIER	silent_mutation	Average:10.967; most accessible tissue: Callus, score: 22.412	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0712961657	NA	1.20E-17	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
vg0712961657	NA	7.72E-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
vg0712961657	NA	4.60E-09	mr1624	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
vg0712961657	1.33E-07	5.36E-06	mr1008_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
vg0712961657	NA	8.41E-06	mr1097_2	Ind_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
vg0712961657	NA	6.86E-06	mr1152_2	Ind_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
vg0712961657	7.47E-07	7.46E-07	mr1261_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
vg0712961657	NA	2.89E-08	mr1624_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
vg0712961657	NA	5.57E-06	mr1741_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
vg0712961657	4.48E-06	1.81E-06	mr1890_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