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Detailed information for vg1117357426:

Variant ID: vg1117357426 (JBrowse)	Variation Type: SNP
Chromosome: chr11	Position: 17357426
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

AGCCGCTCCATCGCAGCCGGCAGCGGCCCCAACTGCACTCGCCGTTGTACAGGCCCAAATCAGCCTTGACCCCGAAGCACAAGCCGAAGCCGACATGGAA[G/A]
CCATGCCGCAGAACATGACACGGCTCCAAGACATGCTTCGCCAAATGCAAGAACAACAACAAGCATACGAGGCGGCAAGGCGGACCAAGGCCACGTTGGC

Reverse complement sequence

GCCAACGTGGCCTTGGTCCGCCTTGCCGCCTCGTATGCTTGTTGTTGTTCTTGCATTTGGCGAAGCATGTCTTGGAGCCGTGTCATGTTCTGCGGCATGG[C/T]
TTCCATGTCGGCTTCGGCTTGTGCTTCGGGGTCAAGGCTGATTTGGGCCTGTACAACGGCGAGTGCAGTTGGGGCCGCTGCCGGCTGCGATGGAGCGGCT

Allele Frequencies:

Populations	Population Size	Frequency of G(primary allele)	Frequency of A(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	61.00%	6.20%	29.24%	3.53%	NA
All Indica	2759	48.30%	9.30%	42.37%	0.04%	NA
All Japonica	1512	86.90%	0.00%	2.38%	10.71%	NA
Aus	269	31.20%	12.30%	56.13%	0.37%	NA
Indica I	595	52.40%	4.40%	43.19%	0.00%	NA
Indica II	465	54.20%	6.70%	39.14%	0.00%	NA
Indica III	913	41.50%	14.90%	43.59%	0.00%	NA
Indica Intermediate	786	49.50%	8.10%	42.24%	0.13%	NA
Temperate Japonica	767	98.00%	0.00%	1.43%	0.52%	NA
Tropical Japonica	504	67.70%	0.00%	4.17%	28.17%	NA
Japonica Intermediate	241	91.70%	0.00%	1.66%	6.64%	NA
VI/Aromatic	96	95.80%	0.00%	4.17%	0.00%	NA
Intermediate	90	70.00%	2.20%	24.44%	3.33%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1117357426	G -> A	LOC_Os11g29880.1	missense_variant ; p.Ala101Thr; MODERATE	nonsynonymous_codon ; A101T	Average:24.365; most accessible tissue: Zhenshan97 panicle, score: 36.038	benign	0.383	TOLERATED	0.06
vg1117357426	G -> DEL	LOC_Os11g29880.1	N	frameshift_variant	Average:24.365; most accessible tissue: Zhenshan97 panicle, score: 36.038	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1117357426	NA	2.84E-06	mr1123_2	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
vg1117357426	1.11E-06	1.11E-06	mr1367_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