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Detailed information for vg0131466658:

Variant ID: vg0131466658 (JBrowse)	Variation Type: SNP
Chromosome: chr01	Position: 31466658
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

GAGCAGTGATGCCCCTGATGAATTTAAGCGCGGAGTGCTTATCGATCTTGATGACCGGATAAGCCTCAGGCCACTTAGTGAACTTGTCGATAGCGACATA[C/T]
AGATACTCGAACCCGTCCGGGGCCCGCCTGAACGGACCCAGGATATCGAGCCCCCAGACAGCAAACGGCCATGAAAGAGGTATGGTCTGCAGGGCCTGGG

Reverse complement sequence

CCCAGGCCCTGCAGACCATACCTCTTTCATGGCCGTTTGCTGTCTGGGGGCTCGATATCCTGGGTCCGTTCAGGCGGGCCCCGGACGGGTTCGAGTATCT[G/A]
TATGTCGCTATCGACAAGTTCACTAAGTGGCCTGAGGCTTATCCGGTCATCAAGATCGATAAGCACTCCGCGCTTAAATTCATCAGGGGCATCACTGCTC

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	32.00%	3.00%	24.31%	40.65%	NA
All Indica	2759	3.40%	4.50%	38.13%	53.93%	NA
All Japonica	1512	83.40%	0.00%	1.52%	15.08%	NA
Aus	269	0.70%	5.90%	24.54%	68.77%	NA
Indica I	595	4.50%	2.70%	18.82%	73.95%	NA
Indica II	465	2.60%	6.50%	13.55%	77.42%	NA
Indica III	913	1.80%	5.70%	62.65%	29.90%	NA
Indica Intermediate	786	5.00%	3.40%	38.80%	52.80%	NA
Temperate Japonica	767	88.00%	0.00%	0.13%	11.86%	NA
Tropical Japonica	504	90.70%	0.00%	2.18%	7.14%	NA
Japonica Intermediate	241	53.50%	0.00%	4.56%	41.91%	NA
VI/Aromatic	96	95.80%	0.00%	0.00%	4.17%	NA
Intermediate	90	72.20%	1.10%	8.89%	17.78%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0131466658	C -> T	LOC_Os01g54690.1	synonymous_variant ; p.Leu1225Leu; LOW	synonymous_codon	Average:28.568; most accessible tissue: Zhenshan97 flag leaf, score: 73.475	N	N	N	N
vg0131466658	C -> DEL	LOC_Os01g54690.1	N	frameshift_variant	Average:28.568; most accessible tissue: Zhenshan97 flag leaf, score: 73.475	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0131466658	5.59E-06	5.59E-06	mr1966_2	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