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Detailed information for vg0628049668:

Variant ID: vg0628049668 (JBrowse)	Variation Type: SNP
Chromosome: chr06	Position: 28049668
Reference Allele: T	Alternative Allele: C
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, others allele: 0.00, population size: 105. )

Flanking Sequence (100 bp) in Reference Genome:

CACGCTGGCTTGTGGTAAGCACGATAAGTTCTTCCAGGGCATCCCGCGAACCGGTCCTTAATCGCCATGGGCACGACTAGCAAAATCATGCACCCACAGC[T/C]
CACCATGTAGTGTATTTTAATTAACCAACACCATAGCGGTGGCGCTAATCCAACAATACCATTAGAACCAACAGTCTAAACATTAATAGGATTCTCCCTA

Reverse complement sequence

TAGGGAGAATCCTATTAATGTTTAGACTGTTGGTTCTAATGGTATTGTTGGATTAGCGCCACCGCTATGGTGTTGGTTAATTAAAATACACTACATGGTG[A/G]
GCTGTGGGTGCATGATTTTGCTAGTCGTGCCCATGGCGATTAAGGACCGGTTCGCGGGATGCCCTGGAAGAACTTATCGTGCTTACCACAAGCCAGCGTG

Allele Frequencies:

Populations	Population Size	Frequency of T(primary allele)	Frequency of C(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	27.90%	6.20%	8.76%	57.22%	NA
All Indica	2759	1.80%	0.30%	13.41%	84.52%	NA
All Japonica	1512	81.00%	12.60%	1.46%	4.89%	NA
Aus	269	0.70%	1.50%	5.95%	91.82%	NA
Indica I	595	1.50%	0.00%	6.72%	91.76%	NA
Indica II	465	3.20%	0.00%	4.73%	92.04%	NA
Indica III	913	1.10%	0.20%	23.11%	75.58%	NA
Indica Intermediate	786	1.90%	0.80%	12.34%	84.99%	NA
Temperate Japonica	767	77.20%	19.40%	0.13%	3.26%	NA
Tropical Japonica	504	82.50%	6.00%	3.97%	7.54%	NA
Japonica Intermediate	241	90.00%	5.00%	0.41%	4.56%	NA
VI/Aromatic	96	14.60%	81.20%	1.04%	3.12%	NA
Intermediate	90	30.00%	11.10%	5.56%	53.33%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0628049668	T -> C	LOC_Os06g46284.1	intron_variant ; MODIFIER	silent_mutation	Average:13.064; most accessible tissue: Zhenshan97 panicle, score: 24.575	N	N	N	N
vg0628049668	T -> C	LOC_Os06g46284.2	intron_variant ; MODIFIER	silent_mutation	Average:13.064; most accessible tissue: Zhenshan97 panicle, score: 24.575	N	N	N	N
vg0628049668	T -> DEL	N	N	silent_mutation	Average:13.064; most accessible tissue: Zhenshan97 panicle, score: 24.575	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0628049668	NA	2.80E-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
vg0628049668	8.31E-09	NA	mr1210	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
vg0628049668	NA	2.11E-07	mr1210	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
vg0628049668	3.45E-06	NA	mr1305	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
vg0628049668	NA	1.27E-11	mr1585	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
vg0628049668	NA	1.27E-06	mr1585	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
vg0628049668	3.89E-09	NA	mr1586	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
vg0628049668	NA	5.50E-08	mr1586	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
vg0628049668	2.04E-06	NA	mr1672	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
vg0628049668	1.69E-06	NA	mr1765	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
vg0628049668	5.95E-06	NA	mr1166_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
vg0628049668	5.47E-07	NA	mr1305_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
vg0628049668	NA	1.93E-06	mr1305_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
vg0628049668	2.40E-06	2.22E-14	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
vg0628049668	NA	1.54E-07	mr1585_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
vg0628049668	1.62E-07	NA	mr1672_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