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Detailed information for vg0209288014:

Variant ID: vg0209288014 (JBrowse)	Variation Type: SNP
Chromosome: chr02	Position: 9288014
Reference Allele: T	Alternative Allele: C
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

CAGTTGCTGTGTGTCTCTGAGATAGTTGAACGAGTGTTGGTCATTCTTCAGAGTTCAGGCTAGCGTGCAAGATGGAGGTAGATGTGTGTCGTTAATGGCT[T/C]
ACGGCATCTGAACTACGATGTACTAAATACTGTTTCAATTGGAAGGAATCGCTCTGCCTCCACGCGTGCTCGTCCGTCGACAATCGGTTCGCCGCCACGC

Reverse complement sequence

GCGTGGCGGCGAACCGATTGTCGACGGACGAGCACGCGTGGAGGCAGAGCGATTCCTTCCAATTGAAACAGTATTTAGTACATCGTAGTTCAGATGCCGT[A/G]
AGCCATTAACGACACACATCTACCTCCATCTTGCACGCTAGCCTGAACTCTGAAGAATGACCAACACTCGTTCAACTATCTCAGAGACACACAGCAACTG

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	49.20%	0.60%	27.80%	22.43%	NA
All Indica	2759	25.30%	0.00%	38.20%	36.53%	NA
All Japonica	1512	94.20%	1.80%	2.78%	1.26%	NA
Aus	269	22.30%	0.00%	71.38%	6.32%	NA
Indica I	595	31.30%	0.00%	14.96%	53.78%	NA
Indica II	465	30.50%	0.00%	43.01%	26.45%	NA
Indica III	913	18.50%	0.00%	51.92%	29.57%	NA
Indica Intermediate	786	25.40%	0.00%	37.02%	37.53%	NA
Temperate Japonica	767	93.40%	2.20%	2.74%	1.69%	NA
Tropical Japonica	504	95.20%	0.80%	3.17%	0.79%	NA
Japonica Intermediate	241	94.60%	2.50%	2.07%	0.83%	NA
VI/Aromatic	96	88.50%	0.00%	11.46%	0.00%	NA
Intermediate	90	64.40%	1.10%	16.67%	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
vg0209288014	T -> DEL	N	N	silent_mutation	Average:33.637; most accessible tissue: Minghui63 panicle, score: 59.629	N	N	N	N
vg0209288014	T -> C	LOC_Os02g16330.1	intron_variant ; MODIFIER	silent_mutation	Average:33.637; most accessible tissue: Minghui63 panicle, score: 59.629	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0209288014	NA	6.58E-08	mr1549_2	Jap_All	Not	Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0209288014	4.26E-06	1.05E-07	mr1550_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
vg0209288014	NA	4.35E-06	mr1757_2	Jap_All	Not	Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251