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Detailed information for vg1128222970:

Variant ID: vg1128222970 (JBrowse)	Variation Type: SNP
Chromosome: chr11	Position: 28222970
Reference Allele: T	Alternative Allele: C
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 1.02, others allele: 0.00, population size: 55. )

Flanking Sequence (100 bp) in Reference Genome:

AGGATGGCGGCCGTCGCGGTCCGGTGTCTCAAAAACAAGGTGGAGAAGAGACCAACCATGGCGGATGTTGTCAAGGAGCTTAAGCAGTTGAGAGAGCAAA[T/C]
ATGCACGCGTGTGTCGTCCTAGATGATCGATTTACACGTACGCCGACTGGATGAATGCAAGCCCGATCTTCAGGTTCTCGGTCAGTTGGTCCGTCGATGA

Reverse complement sequence

TCATCGACGGACCAACTGACCGAGAACCTGAAGATCGGGCTTGCATTCATCCAGTCGGCGTACGTGTAAATCGATCATCTAGGACGACACACGCGTGCAT[A/G]
TTTGCTCTCTCAACTGCTTAAGCTCCTTGACAACATCCGCCATGGTTGGTCTCTTCTCCACCTTGTTTTTGAGACACCGGACCGCGACGGCCGCCATCCT

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	23.60%	7.70%	0.36%	68.32%	NA
All Indica	2759	26.60%	12.10%	0.25%	61.07%	NA
All Japonica	1512	18.80%	1.20%	0.26%	79.70%	NA
Aus	269	19.30%	0.00%	1.86%	78.81%	NA
Indica I	595	36.80%	30.80%	0.00%	32.44%	NA
Indica II	465	2.20%	14.60%	0.22%	83.01%	NA
Indica III	913	37.20%	0.30%	0.22%	62.21%	NA
Indica Intermediate	786	21.00%	10.10%	0.51%	68.45%	NA
Temperate Japonica	767	29.60%	2.00%	0.26%	68.19%	NA
Tropical Japonica	504	4.60%	0.20%	0.20%	95.04%	NA
Japonica Intermediate	241	14.50%	0.80%	0.41%	84.23%	NA
VI/Aromatic	96	18.80%	2.10%	0.00%	79.17%	NA
Intermediate	90	27.80%	14.40%	1.11%	56.67%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1128222970	T -> DEL	LOC_Os11g46950.1	N	frameshift_variant	Average:36.674; most accessible tissue: Callus, score: 85.128	N	N	N	N
vg1128222970	T -> C	LOC_Os11g46950.1	missense_variant ; p.Ile737Thr; MODERATE	nonsynonymous_codon ; I737T	Average:36.674; most accessible tissue: Callus, score: 85.128	unknown	unknown	TOLERATED	0.06

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1128222970	NA	4.64E-06	mr1260_2	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