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Detailed information for vg1128813796:

Variant ID: vg1128813796 (JBrowse)	Variation Type: INDEL
Chromosome: chr11	Position: 28813796
Reference Allele: GTTGAAAATCA	Alternative Allele: G,ATTGAAAATCA
Primary Allele: GTTGAAAATCA	Secondary Allele: G

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

ATCAACGAATCCCCATGGTCAATCTTGAGCTCGCCAATCACTATTAGTGTTCTAAGTGATCCCTGGCCTTGTATGAGTTTCCACTCAAGTTCATCGTTCG[GTTGAAAATCA/G,ATTGAAAATCA]
TTGGTTTCTACAGACAGCCTAAGAAACTTTTGTGATCTAAGTGCACCTTTGCCTCTTTCATCTGAAGTTGAAACTACAAGTGCTTCATCTCTAGAGATAT

Reverse complement sequence

ATATCTCTAGAGATGAAGCACTTGTAGTTTCAACTTCAGATGAAAGAGGCAAAGGTGCACTTAGATCACAAAAGTTTCTTAGGCTGTCTGTAGAAACCAA[TGATTTTCAAC/C,TGATTTTCAAT]
CGAACGATGAACTTGAGTGGAAACTCATACAAGGCCAGGGATCACTTAGAACACTAATAGTGATTGGCGAGCTCAAGATTGACCATGGGGATTCGTTGAT

Allele Frequencies:

Populations	Population Size	Frequency of GTTGAAAATCA(primary allele)	Frequency of G(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	65.20%	1.70%	14.09%	18.60%	ATTGAAAATCA: 0.36%
All Indica	2759	85.00%	1.20%	7.83%	6.02%	NA
All Japonica	1512	30.20%	2.80%	24.54%	41.34%	ATTGAAAATCA: 1.12%
Aus	269	74.00%	1.50%	13.38%	11.15%	NA
Indica I	595	95.50%	0.00%	2.35%	2.18%	NA
Indica II	465	95.50%	0.40%	2.15%	1.94%	NA
Indica III	913	71.50%	2.80%	15.33%	10.30%	NA
Indica Intermediate	786	86.40%	0.60%	6.62%	6.36%	NA
Temperate Japonica	767	49.50%	2.10%	23.60%	22.56%	ATTGAAAATCA: 2.22%
Tropical Japonica	504	9.90%	3.00%	19.44%	67.66%	NA
Japonica Intermediate	241	10.80%	5.00%	38.17%	46.06%	NA
VI/Aromatic	96	17.70%	1.00%	38.54%	42.71%	NA
Intermediate	90	73.30%	1.10%	6.67%	18.89%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1128813796	GTTGAAAATCA -> DEL	LOC_Os11g47780.1	N	frameshift_variant	Average:42.213; most accessible tissue: Callus, score: 66.801	N	N	N	N
vg1128813796	GTTGAAAATCA -> G	LOC_Os11g47780.1	frameshift_variant ; p.Asp546fs; HIGH	frameshift_variant	Average:42.213; most accessible tissue: Callus, score: 66.801	N	N	N	N
vg1128813796	GTTGAAAATCA -> ATTGAAAATCA	LOC_Os11g47780.1	missense_variant ; p.Pro549Ser; MODERATE	nonsynonymous_codon ; P549S	Average:42.213; most accessible tissue: Callus, score: 66.801	benign	+0.470	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1128813796	3.47E-06	3.47E-06	mr1598	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