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Detailed information for vg0515363032:

Variant ID: vg0515363032 (JBrowse)	Variation Type: SNP
Chromosome: chr05	Position: 15363032
Reference Allele: G	Alternative Allele: C
Primary Allele: G	Secondary Allele: C

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

TCTTAACTTCGGCCAGTTCATTTGCTGCCATACGGTAGGGTCGCTTGTACAGGGGAGTGGTTCCTGGAGCAAGATCTATCCGGAACTCAATCTCTCGCTT[G/C]
GGAGGCATACCAGGTAGTTCTTCCTAAAACACGTCTCCGAACTCTCTGACGATGGGGATTTCCGACAGTCTTATCTGATGAAGTTCTGAACTACCGACAG

Reverse complement sequence

CTGTCGGTAGTTCAGAACTTCATCAGATAAGACTGTCGGAAATCCCCATCGTCAGAGAGTTCGGAGACGTGTTTTAGGAAGAACTACCTGGTATGCCTCC[C/G]
AAGCGAGAGATTGAGTTCCGGATAGATCTTGCTCCAGGAACCACTCCCCTGTACAAGCGACCCTACCGTATGGCAGCAAATGAACTGGCCGAAGTTAAGA

Allele Frequencies:

Populations	Population Size	Frequency of G(primary allele)	Frequency of C(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	42.70%	0.50%	26.68%	30.05%	NA
All Indica	2759	24.00%	0.90%	39.83%	35.30%	NA
All Japonica	1512	78.40%	0.00%	0.86%	20.70%	NA
Aus	269	9.30%	0.00%	49.07%	41.64%	NA
Indica I	595	22.00%	0.00%	30.25%	47.73%	NA
Indica II	465	32.50%	0.60%	28.17%	38.71%	NA
Indica III	913	27.60%	1.10%	49.84%	21.47%	NA
Indica Intermediate	786	16.20%	1.50%	42.37%	39.95%	NA
Temperate Japonica	767	94.80%	0.00%	0.65%	4.56%	NA
Tropical Japonica	504	52.40%	0.00%	1.39%	46.23%	NA
Japonica Intermediate	241	80.90%	0.00%	0.41%	18.67%	NA
VI/Aromatic	96	99.00%	0.00%	0.00%	1.04%	NA
Intermediate	90	58.90%	0.00%	18.89%	22.22%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0515363032	G -> DEL	N	N	silent_mutation	Average:9.152; most accessible tissue: Minghui63 young leaf, score: 14.915	N	N	N	N
vg0515363032	G -> C	LOC_Os05g26430.1	downstream_gene_variant ; 1906.0bp to feature; MODIFIER	silent_mutation	Average:9.152; most accessible tissue: Minghui63 young leaf, score: 14.915	N	N	N	N
vg0515363032	G -> C	LOC_Os05g26420.1	intron_variant ; MODIFIER	silent_mutation	Average:9.152; most accessible tissue: Minghui63 young leaf, score: 14.915	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0515363032	3.16E-06	3.16E-06	mr1744_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