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Detailed information for vg0800164289:

Variant ID: vg0800164289 (JBrowse)	Variation Type: SNP
Chromosome: chr08	Position: 164289
Reference Allele: C	Alternative Allele: A
Primary Allele: C	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

CGCCCCGTCCCGTCGGAATGATGAGAGCCTCCAGGCACTCGTCCCTAGCCGGAGCCGGCGTGGGAACTCCTAGAGTTGGCACGTCAGCCCCGGCCAGATA[C/A]
ATTCCAGGCTTCATCGTAACCATTGCAAGGAAGTCATTGTATGAAGAAGGGCAGACGTGTAGCATGCTAAACTGACACGTGGTGGACAAGAATGACCGGT

Reverse complement sequence

ACCGGTCATTCTTGTCCACCACGTGTCAGTTTAGCATGCTACACGTCTGCCCTTCTTCATACAATGACTTCCTTGCAATGGTTACGATGAAGCCTGGAAT[G/T]
TATCTGGCCGGGGCTGACGTGCCAACTCTAGGAGTTCCCACGCCGGCTCCGGCTAGGGACGAGTGCCTGGAGGCTCTCATCATTCCGACGGGACGGGGCG

Allele Frequencies:

Populations	Population Size	Frequency of C(primary allele)	Frequency of A(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	31.30%	2.00%	10.35%	56.41%	NA
All Indica	2759	7.20%	0.10%	11.31%	81.44%	NA
All Japonica	1512	79.80%	5.80%	3.11%	11.31%	NA
Aus	269	7.10%	0.00%	43.87%	49.07%	NA
Indica I	595	13.80%	0.00%	9.24%	76.97%	NA
Indica II	465	3.20%	0.00%	4.73%	92.04%	NA
Indica III	913	4.30%	0.10%	14.90%	80.72%	NA
Indica Intermediate	786	7.90%	0.10%	12.60%	79.39%	NA
Temperate Japonica	767	91.70%	3.40%	2.35%	2.61%	NA
Tropical Japonica	504	66.70%	4.80%	4.17%	24.40%	NA
Japonica Intermediate	241	69.30%	15.80%	3.32%	11.62%	NA
VI/Aromatic	96	15.60%	0.00%	7.29%	77.08%	NA
Intermediate	90	44.40%	3.30%	5.56%	46.67%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0800164289	C -> A	LOC_Os08g01250.1	missense_variant ; p.Met65Ile; MODERATE	nonsynonymous_codon ; M65I	Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125	benign	1.035	TOLERATED	0.61
vg0800164289	C -> DEL	LOC_Os08g01250.1	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
vg0800164289	NA	2.25E-07	mr1118	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
vg0800164289	NA	2.63E-08	mr1123	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
vg0800164289	NA	3.89E-06	mr1150	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
vg0800164289	NA	2.40E-07	mr1240	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
vg0800164289	NA	7.48E-06	mr1242	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
vg0800164289	NA	5.71E-07	mr1495	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
vg0800164289	NA	6.99E-07	mr1496	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
vg0800164289	NA	2.73E-08	mr1693	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
vg0800164289	NA	4.12E-06	mr1936	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
vg0800164289	NA	1.49E-07	mr1961	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
vg0800164289	NA	1.86E-06	mr1113_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
vg0800164289	NA	3.63E-07	mr1118_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
vg0800164289	NA	5.72E-06	mr1240_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