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Detailed information for vg0618322026:

Variant ID: vg0618322026 (JBrowse)	Variation Type: SNP
Chromosome: chr06	Position: 18322026
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

ACGCCGAGTTCTCCTACAATAACAGCTACCAAGCCAGCATACAAATGGCACCCTATGAAGCGTTGTATGGACACAAATGCCGGACACCGCTATTGTGGGA[C/T]
CAAGTTGGGGAAAGCCAAGTGTTCAGGACCGATATCTTGAGAGAAGCTGAAGCGAAGGTCAGAACCATTCAGGATAATCTAAAGGTGGCACAGTCCCAGC

Reverse complement sequence

GCTGGGACTGTGCCACCTTTAGATTATCCTGAATGGTTCTGACCTTCGCTTCAGCTTCTCTCAAGATATCGGTCCTGAACACTTGGCTTTCCCCAACTTG[G/A]
TCCCACAATAGCGGTGTCCGGCATTTGTGTCCATACAACGCTTCATAGGGTGCCATTTGTATGCTGGCTTGGTAGCTGTTATTGTAGGAGAACTCGGCGT

Allele Frequencies:

Populations	Population Size	Frequency of C(primary allele)	Frequency of T(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	61.60%	3.40%	1.95%	32.97%	NA
All Indica	2759	52.60%	4.90%	2.39%	40.09%	NA
All Japonica	1512	82.60%	0.00%	0.26%	17.13%	NA
Aus	269	46.10%	9.30%	7.06%	37.55%	NA
Indica I	595	53.80%	16.10%	2.86%	27.23%	NA
Indica II	465	67.30%	0.20%	1.08%	31.40%	NA
Indica III	913	41.50%	0.30%	2.30%	55.86%	NA
Indica Intermediate	786	56.00%	4.50%	2.93%	36.64%	NA
Temperate Japonica	767	76.70%	0.00%	0.13%	23.21%	NA
Tropical Japonica	504	91.90%	0.00%	0.20%	7.94%	NA
Japonica Intermediate	241	82.20%	0.00%	0.83%	17.01%	NA
VI/Aromatic	96	30.20%	1.00%	2.08%	66.67%	NA
Intermediate	90	65.60%	2.20%	1.11%	31.11%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0618322026	C -> T	LOC_Os06g31480.1	synonymous_variant ; p.Asp1531Asp; LOW	synonymous_codon	Average:8.731; most accessible tissue: Callus, score: 28.865	N	N	N	N
vg0618322026	C -> DEL	LOC_Os06g31480.1	N	frameshift_variant	Average:8.731; most accessible tissue: Callus, score: 28.865	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0618322026	3.66E-06	NA	mr1435	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