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Detailed information for vg0117098473:

Variant ID: vg0117098473 (JBrowse)	Variation Type: SNP
Chromosome: chr01	Position: 17098473
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

GTGCTCCGCAATGAACCATGCTATACAAAAGGTAAAGCCGTTGCCCACGCTGGCTTGTGGTTGGCACGGTTAATGTTTCACAACCGAAACTCGTGAACCG[G/A]
TCCTTAATTGTTATGAGCACGACTCCCAAAACCATGTGCTCACAACCCACCATTATCAAGTTTTAGTTGGCAAGTAATTAATTCACCAATCACGATTGAC

Reverse complement sequence

GTCAATCGTGATTGGTGAATTAATTACTTGCCAACTAAAACTTGATAATGGTGGGTTGTGAGCACATGGTTTTGGGAGTCGTGCTCATAACAATTAAGGA[C/T]
CGGTTCACGAGTTTCGGTTGTGAAACATTAACCGTGCCAACCACAAGCCAGCGTGGGCAACGGCTTTACCTTTTGTATAGCATGGTTCATTGCGGAGCAC

Allele Frequencies:

Populations	Population Size	Frequency of G(primary allele)	Frequency of A(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	32.80%	5.20%	13.92%	48.07%	NA
All Indica	2759	5.70%	0.50%	19.75%	74.05%	NA
All Japonica	1512	78.00%	14.20%	2.98%	4.76%	NA
Aus	269	35.30%	0.40%	20.45%	43.87%	NA
Indica I	595	2.00%	0.30%	6.39%	91.26%	NA
Indica II	465	7.30%	1.10%	13.98%	77.63%	NA
Indica III	913	4.30%	0.00%	34.39%	61.34%	NA
Indica Intermediate	786	9.20%	0.90%	16.28%	73.66%	NA
Temperate Japonica	767	95.30%	0.50%	1.17%	3.00%	NA
Tropical Japonica	504	48.20%	38.70%	5.95%	7.14%	NA
Japonica Intermediate	241	85.50%	6.60%	2.49%	5.39%	NA
VI/Aromatic	96	87.50%	4.20%	2.08%	6.25%	NA
Intermediate	90	40.00%	11.10%	12.22%	36.67%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0117098473	G -> A	LOC_Os01g31260.1	upstream_gene_variant ; 1572.0bp to feature; MODIFIER	silent_mutation	Average:12.09; most accessible tissue: Callus, score: 25.413	N	N	N	N
vg0117098473	G -> A	LOC_Os01g31260-LOC_Os01g31270	intergenic_region ; MODIFIER	silent_mutation	Average:12.09; most accessible tissue: Callus, score: 25.413	N	N	N	N
vg0117098473	G -> DEL	N	N	silent_mutation	Average:12.09; most accessible tissue: Callus, score: 25.413	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0117098473	1.36E-06	NA	mr1188_2	Jap_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