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Detailed information for vg1013723877:

Variant ID: vg1013723877 (JBrowse)	Variation Type: SNP
Chromosome: chr10	Position: 13723877
Reference Allele: G	Alternative Allele: T
Primary Allele: G	Secondary Allele: T

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.00, others allele: 0.00, population size: 309. )

Flanking Sequence (100 bp) in Reference Genome:

TAGCCATATCACTTTTTCAGTGTCCAACAGAAAAGAGAACAAACTTTAATTAAGTGTTTGCCATGTCACCTTTTTAGTGTCCAACAATAAAGACCACATG[G/T]
ATTTTTTTTAGAAACACGGTACAAACGCAAGAGCTCACAACACGCTTAAACTCACCGATCTATAAATGCACACATGCATGCCCTATCCATATATATAAGC

Reverse complement sequence

GCTTATATATATGGATAGGGCATGCATGTGTGCATTTATAGATCGGTGAGTTTAAGCGTGTTGTGAGCTCTTGCGTTTGTACCGTGTTTCTAAAAAAAAT[C/A]
CATGTGGTCTTTATTGTTGGACACTAAAAAGGTGACATGGCAAACACTTAATTAAAGTTTGTTCTCTTTTCTGTTGGACACTGAAAAAGTGATATGGCTA

Allele Frequencies:

Populations	Population Size	Frequency of G(primary allele)	Frequency of T(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	35.40%	6.90%	25.62%	32.08%	NA
All Indica	2759	17.10%	0.10%	34.61%	48.17%	NA
All Japonica	1512	58.00%	21.00%	11.64%	9.33%	NA
Aus	269	95.90%	0.00%	2.60%	1.49%	NA
Indica I	595	10.10%	0.00%	42.69%	47.23%	NA
Indica II	465	11.60%	0.00%	33.55%	54.84%	NA
Indica III	913	24.50%	0.00%	29.79%	45.67%	NA
Indica Intermediate	786	17.00%	0.40%	34.73%	47.84%	NA
Temperate Japonica	767	92.80%	5.10%	1.96%	0.13%	NA
Tropical Japonica	504	11.90%	43.10%	22.02%	23.02%	NA
Japonica Intermediate	241	43.60%	25.70%	20.75%	9.96%	NA
VI/Aromatic	96	29.20%	0.00%	47.92%	22.92%	NA
Intermediate	90	40.00%	7.80%	30.00%	22.22%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1013723877	G -> T	LOC_Os10g26410.1	upstream_gene_variant ; 1145.0bp to feature; MODIFIER	silent_mutation	Average:46.437; most accessible tissue: Zhenshan97 young leaf, score: 73.54	N	N	N	N
vg1013723877	G -> T	LOC_Os10g26410-LOC_Os10g26420	intergenic_region ; MODIFIER	silent_mutation	Average:46.437; most accessible tissue: Zhenshan97 young leaf, score: 73.54	N	N	N	N
vg1013723877	G -> DEL	N	N	silent_mutation	Average:46.437; most accessible tissue: Zhenshan97 young leaf, score: 73.54	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1013723877	NA	2.58E-10	Grain_weight	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
vg1013723877	NA	3.11E-06	mr1248	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
vg1013723877	1.65E-08	5.85E-22	mr1301	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
vg1013723877	NA	2.26E-14	mr1301	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
vg1013723877	5.77E-10	5.72E-19	mr1410	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
vg1013723877	NA	1.13E-14	mr1410	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
vg1013723877	NA	9.95E-11	mr1533	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
vg1013723877	NA	2.42E-09	mr1668	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
vg1013723877	NA	2.59E-06	mr1668	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
vg1013723877	NA	4.54E-12	mr1871	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
vg1013723877	NA	3.01E-07	mr1951	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
vg1013723877	7.42E-09	NA	mr1980	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
vg1013723877	2.13E-06	9.47E-19	mr1980	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
vg1013723877	3.65E-10	8.53E-25	mr1301_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
vg1013723877	NA	3.64E-17	mr1301_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
vg1013723877	9.62E-13	3.37E-22	mr1410_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
vg1013723877	1.28E-06	2.28E-16	mr1410_2	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
vg1013723877	7.11E-09	NA	mr1533_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
vg1013723877	6.13E-07	6.88E-20	mr1533_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
vg1013723877	NA	2.86E-07	mr1668_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
vg1013723877	NA	3.66E-07	mr1980_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