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Detailed information for vg0142242102:

Variant ID: vg0142242102 (JBrowse)	Variation Type: SNP
Chromosome: chr01	Position: 42242102
Reference Allele: G	Alternative Allele: A
Primary Allele: A	Secondary Allele: G

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.99, A: 0.01, others allele: 0.00, population size: 286. )

Flanking Sequence (100 bp) in Reference Genome:

CTCGAGTACATCCTCATTGGTTAGATGGGAGAAATACCAAATTATTACTACTAGAATTTGTGAATAGGTGTTTGTTTATGAGGAGCTGGAAACTGCAGGC[G/A]
GCAAAAATGATGTATGCAACATGAAGCATGTGTGCAACTTTAATTCCAATAATCATATAAAGGAGTTTCCTCCCAAACGATTGTTGTTTCTGTAAAGAAT

Reverse complement sequence

ATTCTTTACAGAAACAACAATCGTTTGGGAGGAAACTCCTTTATATGATTATTGGAATTAAAGTTGCACACATGCTTCATGTTGCATACATCATTTTTGC[C/T]
GCCTGCAGTTTCCAGCTCCTCATAAACAAACACCTATTCACAAATTCTAGTAGTAATAATTTGGTATTTCTCCCATCTAACCAATGAGGATGTACTCGAG

Allele Frequencies:

Populations	Population Size	Frequency of A(primary allele)	Frequency of G(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	67.80%	32.00%	0.13%	0.00%	NA
All Indica	2759	87.60%	12.30%	0.07%	0.00%	NA
All Japonica	1512	35.50%	64.30%	0.20%	0.00%	NA
Aus	269	39.80%	59.90%	0.37%	0.00%	NA
Indica I	595	91.80%	8.20%	0.00%	0.00%	NA
Indica II	465	96.60%	3.40%	0.00%	0.00%	NA
Indica III	913	82.90%	17.10%	0.00%	0.00%	NA
Indica Intermediate	786	84.60%	15.10%	0.25%	0.00%	NA
Temperate Japonica	767	13.60%	86.00%	0.39%	0.00%	NA
Tropical Japonica	504	52.40%	47.60%	0.00%	0.00%	NA
Japonica Intermediate	241	70.10%	29.90%	0.00%	0.00%	NA
VI/Aromatic	96	95.80%	4.20%	0.00%	0.00%	NA
Intermediate	90	58.90%	41.10%	0.00%	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
vg0142242102	G -> A	LOC_Os01g72800.1	upstream_gene_variant ; 4644.0bp to feature; MODIFIER	silent_mutation	Average:62.417; most accessible tissue: Zhenshan97 root, score: 80.208	N	N	N	N
vg0142242102	G -> A	LOC_Os01g72810.1	downstream_gene_variant ; 1535.0bp to feature; MODIFIER	silent_mutation	Average:62.417; most accessible tissue: Zhenshan97 root, score: 80.208	N	N	N	N
vg0142242102	G -> A	LOC_Os01g72820.1	intron_variant ; MODIFIER	silent_mutation	Average:62.417; most accessible tissue: Zhenshan97 root, score: 80.208	N	N	N	N
vg0142242102	G -> A	LOC_Os01g72820.3	intron_variant ; MODIFIER	silent_mutation	Average:62.417; most accessible tissue: Zhenshan97 root, score: 80.208	N	N	N	N
vg0142242102	G -> A	LOC_Os01g72820.4	intron_variant ; MODIFIER	silent_mutation	Average:62.417; most accessible tissue: Zhenshan97 root, score: 80.208	N	N	N	N
vg0142242102	G -> A	LOC_Os01g72820.6	intron_variant ; MODIFIER	silent_mutation	Average:62.417; most accessible tissue: Zhenshan97 root, score: 80.208	N	N	N	N
vg0142242102	G -> A	LOC_Os01g72820.2	intron_variant ; MODIFIER	silent_mutation	Average:62.417; most accessible tissue: Zhenshan97 root, score: 80.208	N	N	N	N
vg0142242102	G -> A	LOC_Os01g72820.5	intron_variant ; MODIFIER	silent_mutation	Average:62.417; most accessible tissue: Zhenshan97 root, score: 80.208	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0142242102	2.21E-06	NA	mr1509_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
vg0142242102	NA	1.27E-06	mr1509_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
vg0142242102	NA	3.70E-06	mr1519_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
vg0142242102	NA	8.28E-06	mr1544_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
vg0142242102	NA	2.49E-06	mr1546_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
vg0142242102	NA	8.76E-06	mr1722_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