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Detailed information for vg0509300373:

Variant ID: vg0509300373 (JBrowse)	Variation Type: SNP
Chromosome: chr05	Position: 9300373
Reference Allele: T	Alternative Allele: C
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

ACATTTACCCCCAAAAAATAGTTTTGCTGAGCATCACTGAATTGAAATTTTAGGTGATACAACAAACAAAATCCAACTGTTTAATATGACTAAAGTGTAG[T/C]
ACTAATTAATATATTCATCAGTTTCATAGAGGCAATAACAAGACAGAAGGAGCAGTACCAGATTTACGCAGTTGTAATCTTCCTCCTTAACCACTTCAGT

Reverse complement sequence

ACTGAAGTGGTTAAGGAGGAAGATTACAACTGCGTAAATCTGGTACTGCTCCTTCTGTCTTGTTATTGCCTCTATGAAACTGATGAATATATTAATTAGT[A/G]
CTACACTTTAGTCATATTAAACAGTTGGATTTTGTTTGTTGTATCACCTAAAATTTCAATTCAGTGATGCTCAGCAAAACTATTTTTTGGGGGTAAATGT

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	96.00%	1.70%	2.33%	0.00%	NA
All Indica	2759	98.30%	0.20%	1.49%	0.00%	NA
All Japonica	1512	90.70%	4.80%	4.50%	0.00%	NA
Aus	269	100.00%	0.00%	0.00%	0.00%	NA
Indica I	595	94.80%	0.50%	4.71%	0.00%	NA
Indica II	465	99.40%	0.00%	0.65%	0.00%	NA
Indica III	913	100.00%	0.00%	0.00%	0.00%	NA
Indica Intermediate	786	98.50%	0.30%	1.27%	0.00%	NA
Temperate Japonica	767	85.10%	7.60%	7.30%	0.00%	NA
Tropical Japonica	504	98.80%	1.00%	0.20%	0.00%	NA
Japonica Intermediate	241	91.30%	4.10%	4.56%	0.00%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	95.60%	3.30%	1.11%	0.00%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0509300373	T -> C	LOC_Os05g16400.1	downstream_gene_variant ; 64.0bp to feature; MODIFIER	silent_mutation	Average:32.948; most accessible tissue: Minghui63 panicle, score: 53.77	N	N	N	N
vg0509300373	T -> C	LOC_Os05g16395-LOC_Os05g16400	intergenic_region ; MODIFIER	silent_mutation	Average:32.948; most accessible tissue: Minghui63 panicle, score: 53.77	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0509300373	4.15E-06	4.15E-06	mr1711_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