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Detailed information for vg0618433395:

Variant ID: vg0618433395 (JBrowse)	Variation Type: SNP
Chromosome: chr06	Position: 18433395
Reference Allele: T	Alternative Allele: C
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

AGAAATTTGTGTGGAGCCCGCAATGCGAGAAAGCGTTCCAAACTCTCAAAGAAAAGCTAGTTTCCTCGCCGGTGTTAATCTTACCGGATACTCGCAAGGA[T/C]
TTCATGGTGTATTGTGACGCTTCGCGCCAAGGATTGGGGTGCGTGCTCATGCAGGAAGGTCATGTGGTAGCCTATGCCTCACGCCAGCTACGGCCCCATG

Reverse complement sequence

CATGGGGCCGTAGCTGGCGTGAGGCATAGGCTACCACATGACCTTCCTGCATGAGCACGCACCCCAATCCTTGGCGCGAAGCGTCACAATACACCATGAA[A/G]
TCCTTGCGAGTATCCGGTAAGATTAACACCGGCGAGGAAACTAGCTTTTCTTTGAGAGTTTGGAACGCTTTCTCGCATTGCGGGCTCCACACAAATTTCT

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	61.00%	2.70%	3.41%	32.86%	NA
All Indica	2759	48.20%	1.40%	3.99%	46.32%	NA
All Japonica	1512	86.80%	0.50%	1.32%	11.44%	NA
Aus	269	63.60%	2.20%	8.55%	25.65%	NA
Indica I	595	52.10%	0.00%	2.18%	45.71%	NA
Indica II	465	49.70%	4.90%	6.88%	38.49%	NA
Indica III	913	42.10%	0.80%	2.96%	54.22%	NA
Indica Intermediate	786	51.70%	1.30%	4.83%	42.24%	NA
Temperate Japonica	767	86.30%	0.00%	0.13%	13.56%	NA
Tropical Japonica	504	87.90%	0.80%	2.38%	8.93%	NA
Japonica Intermediate	241	85.90%	1.20%	2.90%	9.96%	NA
VI/Aromatic	96	14.60%	65.60%	4.17%	15.62%	NA
Intermediate	90	63.30%	12.20%	4.44%	20.00%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0618433395	T -> C	LOC_Os06g31730.1	synonymous_variant ; p.Asp1090Asp; LOW	synonymous_codon	Average:10.791; most accessible tissue: Minghui63 panicle, score: 20.733	N	N	N	N
vg0618433395	T -> DEL	LOC_Os06g31730.1	N	frameshift_variant	Average:10.791; most accessible tissue: Minghui63 panicle, score: 20.733	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0618433395	1.73E-06	1.39E-06	mr1856	Ind_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