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Detailed information for vg1128379239:

Variant ID: vg1128379239 (JBrowse)	Variation Type: SNP
Chromosome: chr11	Position: 28379239
Reference Allele: T	Alternative Allele: C
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.94, T: 0.06, others allele: 0.00, population size: 86. )

Flanking Sequence (100 bp) in Reference Genome:

ATGATATGACTGCACATGTATCGGACTTTGGCATTGCAAGGTTATTGTTAGGTGATGACAGCTCCATGATCTCTGCGAGTATGCCGGGAACAGTTGGGTA[T/C]
ATGGCACCAGGTACTAGCAGCTTCTGTACTCTTGCTCAAAGTAGTGGTATTTTCATAATTATCGTATGGTGCAATCAATAAGCATTGACCAATTTTATTC

Reverse complement sequence

GAATAAAATTGGTCAATGCTTATTGATTGCACCATACGATAATTATGAAAATACCACTACTTTGAGCAAGAGTACAGAAGCTGCTAGTACCTGGTGCCAT[A/G]
TACCCAACTGTTCCCGGCATACTCGCAGAGATCATGGAGCTGTCATCACCTAACAATAACCTTGCAATGCCAAAGTCCGATACATGTGCAGTCATATCAT

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	20.10%	16.50%	9.12%	54.27%	NA
All Indica	2759	20.20%	10.60%	12.90%	56.29%	NA
All Japonica	1512	21.60%	21.90%	2.45%	54.03%	NA
Aus	269	10.00%	27.50%	11.90%	50.56%	NA
Indica I	595	45.00%	3.40%	21.68%	29.92%	NA
Indica II	465	5.80%	7.30%	6.88%	80.00%	NA
Indica III	913	15.30%	13.40%	9.53%	61.77%	NA
Indica Intermediate	786	15.50%	14.90%	13.74%	55.85%	NA
Temperate Japonica	767	31.30%	18.50%	1.69%	48.50%	NA
Tropical Japonica	504	8.90%	28.60%	3.57%	58.93%	NA
Japonica Intermediate	241	17.40%	18.70%	2.49%	61.41%	NA
VI/Aromatic	96	10.40%	64.60%	2.08%	22.92%	NA
Intermediate	90	32.20%	22.20%	4.44%	41.11%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1128379239	T -> DEL	LOC_Os11g47180.1	N	frameshift_variant	Average:49.675; most accessible tissue: Zhenshan97 panicle, score: 65.386	N	N	N	N
vg1128379239	T -> C	LOC_Os11g47180.1	synonymous_variant ; p.Tyr971Tyr; LOW	synonymous_codon	Average:49.675; most accessible tissue: Zhenshan97 panicle, score: 65.386	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1128379239	NA	2.17E-06	mr1376	Ind_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
vg1128379239	NA	5.78E-06	mr1382	Ind_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
vg1128379239	NA	2.17E-06	mr1431	Ind_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
vg1128379239	1.83E-06	1.95E-07	mr1775	Ind_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