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Detailed information for vg0722742982:

Variant ID: vg0722742982 (JBrowse)	Variation Type: SNP
Chromosome: chr07	Position: 22742982
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.99, T: 0.00, others allele: 0.00, population size: 286. )

Flanking Sequence (100 bp) in Reference Genome:

GTGAAGAATTTAGTAGTATCATGACTAAAAGGTTCGAGATGTCTATGATGGGTGAGTTGACCTTCTTCCTCGGGCTACAAGTGAAGCAAGCACAAGAGGG[C/T]
ACTTTCATCTCTCAAACCAAGTACGTGAAGGACATTCTCAAGAAGTTTGGGATGGAAGATGCCAAACCCATCAAGACTCCTATGCCTACTAATGGCCACC

Reverse complement sequence

GGTGGCCATTAGTAGGCATAGGAGTCTTGATGGGTTTGGCATCTTCCATCCCAAACTTCTTGAGAATGTCCTTCACGTACTTGGTTTGAGAGATGAAAGT[G/A]
CCCTCTTGTGCTTGCTTCACTTGTAGCCCGAGGAAGAAGGTCAACTCACCCATCATAGACATCTCGAACCTTTTAGTCATGATACTACTAAATTCTTCAC

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	91.70%	7.50%	0.57%	0.21%	NA
All Indica	2759	93.50%	5.50%	0.62%	0.29%	NA
All Japonica	1512	93.10%	6.50%	0.40%	0.00%	NA
Aus	269	99.30%	0.70%	0.00%	0.00%	NA
Indica I	595	100.00%	0.00%	0.00%	0.00%	NA
Indica II	465	91.40%	8.20%	0.00%	0.43%	NA
Indica III	913	88.40%	9.40%	1.53%	0.66%	NA
Indica Intermediate	786	95.90%	3.70%	0.38%	0.00%	NA
Temperate Japonica	767	88.40%	11.00%	0.65%	0.00%	NA
Tropical Japonica	504	99.80%	0.20%	0.00%	0.00%	NA
Japonica Intermediate	241	94.20%	5.40%	0.41%	0.00%	NA
VI/Aromatic	96	5.20%	90.60%	2.08%	2.08%	NA
Intermediate	90	81.10%	16.70%	2.22%	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
vg0722742982	C -> DEL	LOC_Os07g37900.1	N	frameshift_variant	Average:19.157; most accessible tissue: Zhenshan97 root, score: 27.411	N	N	N	N
vg0722742982	C -> T	LOC_Os07g37900.1	synonymous_variant ; p.Gly1381Gly; LOW	synonymous_codon	Average:19.157; most accessible tissue: Zhenshan97 root, score: 27.411	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0722742982	NA	5.08E-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
vg0722742982	NA	4.89E-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
vg0722742982	NA	8.24E-07	mr1071	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
vg0722742982	NA	8.01E-06	mr1080	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
vg0722742982	NA	5.66E-06	mr1140	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
vg0722742982	NA	5.27E-06	mr1203	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
vg0722742982	NA	4.15E-06	mr1395	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
vg0722742982	1.23E-06	1.23E-06	mr1609	Jap_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
vg0722742982	NA	3.84E-06	mr1618	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
vg0722742982	NA	8.66E-07	mr1619	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
vg0722742982	NA	9.31E-09	mr1829	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
vg0722742982	NA	5.14E-06	mr1900	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
vg0722742982	NA	2.68E-07	mr1057_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
vg0722742982	NA	6.69E-06	mr1057_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
vg0722742982	NA	2.07E-08	mr1585_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
vg0722742982	NA	3.09E-14	mr1829_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