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Detailed information for vg0428135712:

Variant ID: vg0428135712 (JBrowse)	Variation Type: SNP
Chromosome: chr04	Position: 28135712
Reference Allele: T	Alternative Allele: C
Primary Allele: C	Secondary Allele: T

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

Flanking Sequence (100 bp) in Reference Genome:

GTTGAAGATCTGAATGTCTTATGTGTCATAAATACACAAACCAACCGTGATCCAGGGTTTACTACTTCGGTATGCACAAAGCTACTGCATGCAGGGGCGC[T/C]
AGGAGGGGGGTGGGGGCTGAAATTTTGGAATGAAAAAAGTGAAAACTGAGCAACTTTTGACTAAATTTGAATAATTCACAAAGAAAAACAAATGAAAAAG

Reverse complement sequence

CTTTTTCATTTGTTTTTCTTTGTGAATTATTCAAATTTAGTCAAAAGTTGCTCAGTTTTCACTTTTTTCATTCCAAAATTTCAGCCCCCACCCCCCTCCT[A/G]
GCGCCCCTGCATGCAGTAGCTTTGTGCATACCGAAGTAGTAAACCCTGGATCACGGTTGGTTTGTGTATTTATGACACATAAGACATTCAGATCTTCAAC

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	66.30%	32.20%	1.54%	0.00%	NA
All Indica	2759	94.50%	5.10%	0.40%	0.00%	NA
All Japonica	1512	14.60%	81.80%	3.57%	0.00%	NA
Aus	269	96.70%	1.50%	1.86%	0.00%	NA
Indica I	595	97.50%	1.70%	0.84%	0.00%	NA
Indica II	465	95.90%	3.70%	0.43%	0.00%	NA
Indica III	913	90.90%	9.00%	0.11%	0.00%	NA
Indica Intermediate	786	95.70%	3.90%	0.38%	0.00%	NA
Temperate Japonica	767	8.10%	86.20%	5.74%	0.00%	NA
Tropical Japonica	504	29.20%	68.80%	1.98%	0.00%	NA
Japonica Intermediate	241	5.00%	95.00%	0.00%	0.00%	NA
VI/Aromatic	96	3.10%	96.90%	0.00%	0.00%	NA
Intermediate	90	45.60%	51.10%	3.33%	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
vg0428135712	T -> C	LOC_Os04g47420.1	downstream_gene_variant ; 2021.0bp to feature; MODIFIER	silent_mutation	Average:56.397; most accessible tissue: Callus, score: 79.22	N	N	N	N
vg0428135712	T -> C	LOC_Os04g47410.1	intron_variant ; MODIFIER	silent_mutation	Average:56.397; most accessible tissue: Callus, score: 79.22	N	N	N	N
vg0428135712	T -> C	LOC_Os04g47410.4	intron_variant ; MODIFIER	silent_mutation	Average:56.397; most accessible tissue: Callus, score: 79.22	N	N	N	N
vg0428135712	T -> C	LOC_Os04g47410.3	intron_variant ; MODIFIER	silent_mutation	Average:56.397; most accessible tissue: Callus, score: 79.22	N	N	N	N
vg0428135712	T -> C	LOC_Os04g47410.5	intron_variant ; MODIFIER	silent_mutation	Average:56.397; most accessible tissue: Callus, score: 79.22	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0428135712	NA	3.75E-12	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
vg0428135712	NA	4.71E-07	mr1781	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
vg0428135712	NA	2.56E-21	mr1010_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
vg0428135712	NA	3.67E-15	mr1035_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
vg0428135712	NA	1.95E-07	mr1045_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
vg0428135712	NA	6.76E-06	mr1051_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
vg0428135712	NA	8.10E-07	mr1053_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
vg0428135712	NA	2.19E-23	mr1077_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
vg0428135712	NA	7.59E-06	mr1092_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
vg0428135712	7.28E-06	NA	mr1220_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
vg0428135712	NA	1.99E-08	mr1220_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
vg0428135712	NA	3.93E-07	mr1252_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
vg0428135712	NA	8.00E-07	mr1252_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
vg0428135712	NA	7.33E-06	mr1263_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
vg0428135712	NA	2.96E-08	mr1299_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
vg0428135712	NA	3.20E-08	mr1482_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
vg0428135712	NA	1.15E-13	mr1537_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
vg0428135712	NA	3.73E-17	mr1592_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
vg0428135712	NA	5.56E-19	mr1637_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
vg0428135712	NA	7.78E-15	mr1713_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
vg0428135712	NA	7.54E-07	mr1727_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
vg0428135712	NA	1.80E-09	mr1741_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
vg0428135712	NA	5.80E-13	mr1770_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
vg0428135712	NA	5.52E-10	mr1783_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
vg0428135712	NA	6.75E-08	mr1785_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
vg0428135712	NA	1.23E-09	mr1804_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
vg0428135712	NA	4.96E-08	mr1837_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
vg0428135712	NA	5.79E-14	mr1938_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
vg0428135712	NA	7.82E-06	mr1982_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