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Detailed information for vg0101949068:

Variant ID: vg0101949068 (JBrowse)	Variation Type: SNP
Chromosome: chr01	Position: 1949068
Reference Allele: A	Alternative Allele: G
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 1.00, others allele: 0.00, population size: 250. )

Flanking Sequence (100 bp) in Reference Genome:

CATGACTTCTTCCCTCACCGATCACATCTTCAGGAGCTTAACCGGAGATCTCAATGGCCTTCACCTCAGGCTTCTTGACCTCGGCCTTGGGCACGGTGAC[A/G]
GTGAGCACGCCGTTCTCCAGTCCGGCCTTCACCTGGTCCACCTTGGCGTTCTCCGGCAGCCTGAACCGCCGCATGAACTGCCCGCTGCTGCGCTCCACGC

Reverse complement sequence

GCGTGGAGCGCAGCAGCGGGCAGTTCATGCGGCGGTTCAGGCTGCCGGAGAACGCCAAGGTGGACCAGGTGAAGGCCGGACTGGAGAACGGCGTGCTCAC[T/C]
GTCACCGTGCCCAAGGCCGAGGTCAAGAAGCCTGAGGTGAAGGCCATTGAGATCTCCGGTTAAGCTCCTGAAGATGTGATCGGTGAGGGAAGAAGTCATG

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	58.80%	41.00%	0.04%	0.23%	NA
All Indica	2759	85.10%	14.50%	0.04%	0.40%	NA
All Japonica	1512	24.10%	75.90%	0.00%	0.00%	NA
Aus	269	4.10%	95.90%	0.00%	0.00%	NA
Indica I	595	97.30%	2.50%	0.00%	0.17%	NA
Indica II	465	94.20%	5.60%	0.00%	0.22%	NA
Indica III	913	76.20%	23.30%	0.11%	0.33%	NA
Indica Intermediate	786	80.80%	18.40%	0.00%	0.76%	NA
Temperate Japonica	767	15.50%	84.50%	0.00%	0.00%	NA
Tropical Japonica	504	45.00%	55.00%	0.00%	0.00%	NA
Japonica Intermediate	241	7.50%	92.50%	0.00%	0.00%	NA
VI/Aromatic	96	4.20%	95.80%	0.00%	0.00%	NA
Intermediate	90	55.60%	43.30%	1.11%	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
vg0101949068	A -> G	LOC_Os01g04370.1	synonymous_variant ; p.Thr130Thr; LOW	synonymous_codon	Average:74.786; most accessible tissue: Zhenshan97 flower, score: 88.571	N	N	N	N
vg0101949068	A -> DEL	LOC_Os01g04370.1	N	frameshift_variant	Average:74.786; most accessible tissue: Zhenshan97 flower, score: 88.571	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0101949068	NA	1.31E-06	Yield	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
vg0101949068	NA	1.37E-09	mr1465	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
vg0101949068	NA	9.69E-07	mr1925	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
vg0101949068	NA	1.53E-10	mr1228_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
vg0101949068	NA	3.96E-23	mr1401_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