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Detailed information for vg0721979371:

Variant ID: vg0721979371 (JBrowse)	Variation Type: SNP
Chromosome: chr07	Position: 21979371
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

GTCGTCGGTTGTATTCTCGGGCTGTCTGAGCTGCAACCTAAGTTAAGGTAAATAAGTCCTCTATTTATTTTAAGGATTGTTATGATTCATATTTGTCACC[G/A]
TGGGTACCAGCACTATGTCCTGGGACTGGTACCGAGATCGCGGTTTCGTAGGAAGCGGTTCGCGCCGCTTTCCCTACGACACGCTCCTGTCAGGTGCCGT

Reverse complement sequence

ACGGCACCTGACAGGAGCGTGTCGTAGGGAAAGCGGCGCGAACCGCTTCCTACGAAACCGCGATCTCGGTACCAGTCCCAGGACATAGTGCTGGTACCCA[C/T]
GGTGACAAATATGAATCATAACAATCCTTAAAATAAATAGAGGACTTATTTACCTTAACTTAGGTTGCAGCTCAGACAGCCCGAGAATACAACCGACGAC

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	41.60%	4.90%	22.05%	31.46%	NA
All Indica	2759	16.70%	0.30%	31.24%	51.83%	NA
All Japonica	1512	83.70%	14.40%	1.19%	0.66%	NA
Aus	269	56.90%	0.00%	40.15%	2.97%	NA
Indica I	595	4.40%	0.20%	13.11%	82.35%	NA
Indica II	465	21.10%	0.20%	29.25%	49.46%	NA
Indica III	913	17.70%	0.40%	45.02%	36.80%	NA
Indica Intermediate	786	22.10%	0.10%	30.15%	47.58%	NA
Temperate Japonica	767	94.80%	3.90%	0.26%	1.04%	NA
Tropical Japonica	504	70.00%	28.60%	1.39%	0.00%	NA
Japonica Intermediate	241	77.20%	18.30%	3.73%	0.83%	NA
VI/Aromatic	96	41.70%	0.00%	34.38%	23.96%	NA
Intermediate	90	51.10%	7.80%	23.33%	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
vg0721979371	G -> DEL	N	N	silent_mutation	Average:11.839; most accessible tissue: Minghui63 young leaf, score: 21.268	N	N	N	N
vg0721979371	G -> A	LOC_Os07g36690-LOC_Os07g36700	intergenic_region ; MODIFIER	silent_mutation	Average:11.839; most accessible tissue: Minghui63 young leaf, score: 21.268	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0721979371	NA	4.30E-06	mr1086	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
vg0721979371	NA	2.51E-08	mr1104	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
vg0721979371	NA	9.07E-06	mr1139	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
vg0721979371	3.61E-06	9.65E-08	mr1155	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
vg0721979371	NA	1.66E-09	mr1213	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
vg0721979371	NA	5.00E-08	mr1224	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
vg0721979371	NA	3.33E-07	mr1225	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
vg0721979371	2.35E-07	8.68E-06	mr1226	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
vg0721979371	NA	7.86E-06	mr1246	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
vg0721979371	NA	8.48E-07	mr1411	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
vg0721979371	6.13E-06	1.27E-08	mr1437	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
vg0721979371	NA	1.09E-07	mr1620	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
vg0721979371	NA	7.58E-07	mr1668	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
vg0721979371	NA	1.92E-06	mr1790	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
vg0721979371	2.51E-06	3.29E-06	mr1878	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