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Detailed information for vg0107138425:

Variant ID: vg0107138425 (JBrowse)	Variation Type: SNP
Chromosome: chr01	Position: 7138425
Reference Allele: A	Alternative Allele: G
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

TTTTCATTGTTGTTAGATGATAAAACATGATTAATACTTTATGCATGTCTTATCTTTTTAATTTTTTTTAAATAAGACGGAGGGTCAAACGTTGGACACG[A/G]
AAACCCAGGGTTTGTCTTTTTTTTAGGACAGAGGGATTACGTAGCAAGACTATTTACGACCTTTTTATCCATACATCCACGATAGGAACTTGCAACTGGA

Reverse complement sequence

TCCAGTTGCAAGTTCCTATCGTGGATGTATGGATAAAAAGGTCGTAAATAGTCTTGCTACGTAATCCCTCTGTCCTAAAAAAAAGACAAACCCTGGGTTT[T/C]
CGTGTCCAACGTTTGACCCTCCGTCTTATTTAAAAAAAATTAAAAAGATAAGACATGCATAAAGTATTAATCATGTTTTATCATCTAACAACAATGAAAA

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	71.40%	28.30%	0.15%	0.17%	NA
All Indica	2759	97.40%	2.10%	0.22%	0.29%	NA
All Japonica	1512	18.50%	81.50%	0.00%	0.00%	NA
Aus	269	100.00%	0.00%	0.00%	0.00%	NA
Indica I	595	99.20%	0.70%	0.00%	0.17%	NA
Indica II	465	99.40%	0.40%	0.00%	0.22%	NA
Indica III	913	97.80%	1.20%	0.44%	0.55%	NA
Indica Intermediate	786	94.40%	5.20%	0.25%	0.13%	NA
Temperate Japonica	767	2.10%	97.90%	0.00%	0.00%	NA
Tropical Japonica	504	48.00%	52.00%	0.00%	0.00%	NA
Japonica Intermediate	241	8.70%	91.30%	0.00%	0.00%	NA
VI/Aromatic	96	78.10%	21.90%	0.00%	0.00%	NA
Intermediate	90	70.00%	28.90%	1.11%	0.00%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0107138425	A -> G	LOC_Os01g12880.1	downstream_gene_variant ; 1095.0bp to feature; MODIFIER	silent_mutation	Average:77.038; most accessible tissue: Zhenshan97 flower, score: 88.302	N	N	N	N
vg0107138425	A -> G	LOC_Os01g12880-LOC_Os01g12890	intergenic_region ; MODIFIER	silent_mutation	Average:77.038; most accessible tissue: Zhenshan97 flower, score: 88.302	N	N	N	N
vg0107138425	A -> DEL	N	N	silent_mutation	Average:77.038; most accessible tissue: Zhenshan97 flower, score: 88.302	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0107138425	NA	4.23E-09	mr1005	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
vg0107138425	NA	4.29E-58	mr1019	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
vg0107138425	NA	7.47E-07	mr1364	Jap_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
vg0107138425	NA	2.69E-07	mr1443	Jap_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
vg0107138425	NA	3.69E-09	mr1575	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
vg0107138425	NA	1.69E-14	mr1653	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
vg0107138425	NA	9.55E-84	mr1672	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
vg0107138425	NA	4.84E-40	mr1243_2	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
vg0107138425	5.60E-08	NA	mr1498_2	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
vg0107138425	4.34E-09	3.76E-11	mr1498_2	Jap_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
vg0107138425	NA	6.64E-25	mr1653_2	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
vg0107138425	NA	7.63E-69	mr1733_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
vg0107138425	NA	1.07E-09	mr1947_2	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