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Detailed information for vg1005036154:

Variant ID: vg1005036154 (JBrowse)	Variation Type: SNP
Chromosome: chr10	Position: 5036154
Reference Allele: T	Alternative Allele: C
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

CTGACAAGCATGACTATACTTTCTTCCCCCAGCTTCAAACTTTATCGACAGAAGGTCTTCTCGATCACTAGTCAACGTCACGCGAACACGACACTTCTCC[T/C]
CGTTGGGGTCATAGGGAATCTGGCGATACTCAGGGGCAACGTCGTAGCCTACTTCAAATGCCATCATTCTCAGCTCCCTGACGAATCCTACCGCATTGAT

Reverse complement sequence

ATCAATGCGGTAGGATTCGTCAGGGAGCTGAGAATGATGGCATTTGAAGTAGGCTACGACGTTGCCCCTGAGTATCGCCAGATTCCCTATGACCCCAACG[A/G]
GGAGAAGTGTCGTGTTCGCGTGACGTTGACTAGTGATCGAGAAGACCTTCTGTCGATAAAGTTTGAAGCTGGGGGAAGAAAGTATAGTCATGCTTGTCAG

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	86.20%	4.90%	1.71%	7.17%	NA
All Indica	2759	84.90%	8.10%	2.68%	4.31%	NA
All Japonica	1512	85.30%	0.30%	0.26%	14.09%	NA
Aus	269	99.30%	0.00%	0.37%	0.37%	NA
Indica I	595	95.00%	3.40%	1.51%	0.17%	NA
Indica II	465	84.50%	3.20%	2.37%	9.89%	NA
Indica III	913	77.10%	13.00%	2.96%	6.90%	NA
Indica Intermediate	786	86.50%	8.90%	3.44%	1.15%	NA
Temperate Japonica	767	85.90%	0.30%	0.26%	13.56%	NA
Tropical Japonica	504	85.70%	0.20%	0.40%	13.69%	NA
Japonica Intermediate	241	82.60%	0.80%	0.00%	16.60%	NA
VI/Aromatic	96	97.90%	0.00%	1.04%	1.04%	NA
Intermediate	90	91.10%	2.20%	1.11%	5.56%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1005036154	T -> C	LOC_Os10g09310.1	missense_variant ; p.Glu22Gly; MODERATE	nonsynonymous_codon ; E22G	Average:39.071; most accessible tissue: Zhenshan97 flag leaf, score: 61.322	unknown	unknown	DELETERIOUS	0.00
vg1005036154	T -> DEL	LOC_Os10g09310.1	N	frameshift_variant	Average:39.071; most accessible tissue: Zhenshan97 flag leaf, score: 61.322	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1005036154	6.51E-07	6.51E-07	mr1584	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