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Detailed information for vg1103727229:

Variant ID: vg1103727229 (JBrowse)	Variation Type: SNP
Chromosome: chr11	Position: 3727229
Reference Allele: C	Alternative Allele: G
Primary Allele: C	Secondary Allele: G

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, others allele: 0.00, population size: 107. )

Flanking Sequence (100 bp) in Reference Genome:

ATGGTCTCGAGTTCATGACATGTGGGCCCCACTTGTTATTAGCTCTTCCTATTTCCCTTTAGAAAATAATTCGGTAGGAAAAAGGAATAAACCCGGGGTC[C/G]
CACTTGTCAATGGATATGTCTTGGATTAAAAATAAATCGTTTATGAACAGTAGCTTTTCGCAATTTCTCGGATTAATTCAAAGTTGAATCTTTACACTAG

Reverse complement sequence

CTAGTGTAAAGATTCAACTTTGAATTAATCCGAGAAATTGCGAAAAGCTACTGTTCATAAACGATTTATTTTTAATCCAAGACATATCCATTGACAAGTG[G/C]
GACCCCGGGTTTATTCCTTTTTCCTACCGAATTATTTTCTAAAGGGAAATAGGAAGAGCTAATAACAAGTGGGGCCCACATGTCATGAACTCGAGACCAT

Allele Frequencies:

Populations	Population Size	Frequency of C(primary allele)	Frequency of G(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	70.60%	0.10%	5.18%	24.10%	NA
All Indica	2759	66.00%	0.20%	6.09%	27.73%	NA
All Japonica	1512	82.30%	0.00%	1.72%	16.01%	NA
Aus	269	62.10%	0.00%	16.73%	21.19%	NA
Indica I	595	40.80%	0.00%	3.03%	56.13%	NA
Indica II	465	77.60%	0.00%	3.01%	19.35%	NA
Indica III	913	76.00%	0.50%	11.72%	11.72%	NA
Indica Intermediate	786	66.40%	0.10%	3.69%	29.77%	NA
Temperate Japonica	767	99.20%	0.00%	0.13%	0.65%	NA
Tropical Japonica	504	52.40%	0.00%	4.56%	43.06%	NA
Japonica Intermediate	241	90.90%	0.00%	0.83%	8.30%	NA
VI/Aromatic	96	39.60%	0.00%	2.08%	58.33%	NA
Intermediate	90	74.40%	0.00%	4.44%	21.11%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1103727229	C -> DEL	N	N	silent_mutation	Average:8.22; most accessible tissue: Callus, score: 30.801	N	N	N	N
vg1103727229	C -> G	LOC_Os11g07400.1	upstream_gene_variant ; 3626.0bp to feature; MODIFIER	silent_mutation	Average:8.22; most accessible tissue: Callus, score: 30.801	N	N	N	N
vg1103727229	C -> G	LOC_Os11g07400-LOC_Os11g07410	intergenic_region ; MODIFIER	silent_mutation	Average:8.22; most accessible tissue: Callus, score: 30.801	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1103727229	NA	7.85E-08	mr1348_2	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
vg1103727229	NA	3.24E-06	mr1348_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