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Detailed information for vg0900240275:

Variant ID: vg0900240275 (JBrowse)	Variation Type: SNP
Chromosome: chr09	Position: 240275
Reference Allele: A	Alternative Allele: G
Primary Allele: A	Secondary Allele: G

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

TCTTGACAGAAAAGCTACGTAGATAACCGCCGAAGGGAGCTTGCTTTTGAAGCAGGGGATTATGTGTATCTCCATGTCACTCCGCTCAGGGGAGTACACC[A/G]
TTTCCAAACCAAAGGAAAGTTGGCACCACGCTTTGTGGGACCATATTGGATTTTGGAACGCAGGGGTGAAGTTGCTTACCAGCTTGAGCTTCCCTCCAAC

Reverse complement sequence

GTTGGAGGGAAGCTCAAGCTGGTAAGCAACTTCACCCCTGCGTTCCAAAATCCAATATGGTCCCACAAAGCGTGGTGCCAACTTTCCTTTGGTTTGGAAA[T/C]
GGTGTACTCCCCTGAGCGGAGTGACATGGAGATACACATAATCCCCTGCTTCAAAAGCAAGCTCCCTTCGGCGGTTATCTACGTAGCTTTTCTGTCAAGA

Allele Frequencies:

Populations	Population Size	Frequency of A(primary allele)	Frequency of G(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	37.10%	4.00%	28.23%	30.70%	NA
All Indica	2759	7.00%	5.80%	39.14%	48.13%	NA
All Japonica	1512	91.60%	0.40%	6.81%	1.19%	NA
Aus	269	9.70%	7.80%	51.67%	30.86%	NA
Indica I	595	9.40%	0.70%	36.64%	53.28%	NA
Indica II	465	4.90%	4.90%	37.20%	52.90%	NA
Indica III	913	4.60%	9.90%	43.81%	41.73%	NA
Indica Intermediate	786	9.00%	5.30%	36.77%	48.85%	NA
Temperate Japonica	767	86.40%	0.80%	12.39%	0.39%	NA
Tropical Japonica	504	97.20%	0.00%	0.40%	2.38%	NA
Japonica Intermediate	241	96.30%	0.00%	2.49%	1.24%	NA
VI/Aromatic	96	94.80%	0.00%	1.04%	4.17%	NA
Intermediate	90	63.30%	4.40%	12.22%	20.00%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0900240275	A -> G	LOC_Os09g01280.1	missense_variant ; p.His430Arg; MODERATE	nonsynonymous_codon ; H430R	Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125	benign	-0.86	TOLERATED	1.00
vg0900240275	A -> DEL	LOC_Os09g01280.1	N	frameshift_variant	Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0900240275	NA	1.58E-16	mr1062	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
vg0900240275	NA	6.90E-08	mr1062	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
vg0900240275	1.72E-07	1.72E-07	mr1166	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
vg0900240275	NA	3.86E-08	mr1210	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
vg0900240275	NA	1.65E-08	mr1305	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
vg0900240275	6.66E-06	6.66E-06	mr1409	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
vg0900240275	NA	1.59E-06	mr1420	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
vg0900240275	NA	1.21E-06	mr1508	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
vg0900240275	NA	3.80E-08	mr1515	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
vg0900240275	NA	5.21E-09	mr1585	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
vg0900240275	NA	1.49E-08	mr1586	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
vg0900240275	5.09E-06	5.09E-06	mr1649	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
vg0900240275	NA	1.85E-09	mr1765	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