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Detailed information for vg1227422436:

Variant ID: vg1227422436 (JBrowse)	Variation Type: SNP
Chromosome: chr12	Position: 27422436
Reference Allele: T	Alternative Allele: C
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

GTGAGTTCTAGTATTTTCATGCATGTACCAGTACTAGTTGTGTTCAGAAAAGTTCCTAGCCATCCTATAAATAGGCAGCTATGTCCTAGATGTGATGCTG[T/C]
TGTCCAACAATCAATGTAACGTGCAATACTTGAGCAAAGCATAACCAGTTTGTCAAACAAACACAGAGCTTCTCTCCTCTGTTCTCCTTCTCTGTTCCAT

Reverse complement sequence

ATGGAACAGAGAAGGAGAACAGAGGAGAGAAGCTCTGTGTTTGTTTGACAAACTGGTTATGCTTTGCTCAAGTATTGCACGTTACATTGATTGTTGGACA[A/G]
CAGCATCACATCTAGGACATAGCTGCCTATTTATAGGATGGCTAGGAACTTTTCTGAACACAACTAGTACTGGTACATGCATGAAAATACTAGAACTCAC

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	27.40%	7.30%	10.64%	54.66%	NA
All Indica	2759	2.00%	0.50%	10.91%	86.52%	NA
All Japonica	1512	77.40%	18.30%	3.64%	0.66%	NA
Aus	269	1.50%	0.40%	45.72%	52.42%	NA
Indica I	595	1.00%	0.20%	9.58%	89.24%	NA
Indica II	465	2.20%	0.00%	24.30%	73.55%	NA
Indica III	913	2.10%	0.80%	3.94%	93.21%	NA
Indica Intermediate	786	2.70%	0.90%	12.09%	84.35%	NA
Temperate Japonica	767	78.20%	15.90%	5.48%	0.39%	NA
Tropical Japonica	504	83.10%	15.30%	0.79%	0.79%	NA
Japonica Intermediate	241	63.10%	32.00%	3.73%	1.24%	NA
VI/Aromatic	96	26.00%	54.20%	9.38%	10.42%	NA
Intermediate	90	41.10%	3.30%	16.67%	38.89%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1227422436	T -> C	LOC_Os12g44210.1	5_prime_UTR_premature_start_codon_gain_variant ; LOW	silent_mutation	Average:44.798; most accessible tissue: Zhenshan97 root, score: 68.289	N	N	N	N
vg1227422436	T -> C	LOC_Os12g44210.1	5_prime_UTR_variant ; 250.0bp to feature; MODIFIER	silent_mutation	Average:44.798; most accessible tissue: Zhenshan97 root, score: 68.289	N	N	N	N
vg1227422436	T -> C	LOC_Os12g44220.1	upstream_gene_variant ; 3874.0bp to feature; MODIFIER	silent_mutation	Average:44.798; most accessible tissue: Zhenshan97 root, score: 68.289	N	N	N	N
vg1227422436	T -> C	LOC_Os12g44220.2	upstream_gene_variant ; 3874.0bp to feature; MODIFIER	silent_mutation	Average:44.798; most accessible tissue: Zhenshan97 root, score: 68.289	N	N	N	N
vg1227422436	T -> C	LOC_Os12g44200.1	downstream_gene_variant ; 249.0bp to feature; MODIFIER	silent_mutation	Average:44.798; most accessible tissue: Zhenshan97 root, score: 68.289	N	N	N	N
vg1227422436	T -> DEL	N	N	silent_mutation	Average:44.798; most accessible tissue: Zhenshan97 root, score: 68.289	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1227422436	5.58E-07	NA	mr1679	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
vg1227422436	NA	9.45E-06	mr1691	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
vg1227422436	NA	8.08E-08	mr1829	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
vg1227422436	5.54E-07	NA	mr1679_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
vg1227422436	NA	4.09E-07	mr1679_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
vg1227422436	NA	5.10E-10	mr1829_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