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Detailed information for vg0322639869:

Variant ID: vg0322639869 (JBrowse)	Variation Type: SNP
Chromosome: chr03	Position: 22639869
Reference Allele: C	Alternative Allele: A
Primary Allele: C	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

CCATAGAGAGGGATGTCCCCTCTTTACTTACATCTCATCTAAATAGTTATCAATTTTTTTAAATAAAATAACAACATATATTAATATAAAATATATATCA[C/A]
TCCATAAATATGCAGAGCAAATTTAACTTCTACAAGTTACAACGAAAAGAACAAAATAAACTGAAAATAGTTATCTATCGTACATTCGCAGCTATATTTG

Reverse complement sequence

CAAATATAGCTGCGAATGTACGATAGATAACTATTTTCAGTTTATTTTGTTCTTTTCGTTGTAACTTGTAGAAGTTAAATTTGCTCTGCATATTTATGGA[G/T]
TGATATATATTTTATATTAATATATGTTGTTATTTTATTTAAAAAAATTGATAACTATTTAGATGAGATGTAAGTAAAGAGGGGACATCCCTCTCTATGG

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	56.90%	5.00%	9.75%	28.33%	NA
All Indica	2759	36.70%	0.90%	16.42%	45.99%	NA
All Japonica	1512	99.80%	0.00%	0.00%	0.20%	NA
Aus	269	2.20%	76.60%	0.00%	21.19%	NA
Indica I	595	3.20%	0.00%	31.60%	65.21%	NA
Indica II	465	74.40%	0.00%	5.38%	20.22%	NA
Indica III	913	38.10%	0.40%	13.36%	48.08%	NA
Indica Intermediate	786	38.00%	2.70%	15.01%	44.27%	NA
Temperate Japonica	767	100.00%	0.00%	0.00%	0.00%	NA
Tropical Japonica	504	99.60%	0.00%	0.00%	0.40%	NA
Japonica Intermediate	241	99.60%	0.00%	0.00%	0.41%	NA
VI/Aromatic	96	95.80%	4.20%	0.00%	0.00%	NA
Intermediate	90	77.80%	2.20%	8.89%	11.11%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0322639869	C -> A	LOC_Os03g40720.1	downstream_gene_variant ; 1583.0bp to feature; MODIFIER	silent_mutation	Average:64.814; most accessible tissue: Zhenshan97 root, score: 81.564	N	N	N	N
vg0322639869	C -> A	LOC_Os03g40710.1	intron_variant ; MODIFIER	silent_mutation	Average:64.814; most accessible tissue: Zhenshan97 root, score: 81.564	N	N	N	N
vg0322639869	C -> DEL	N	N	silent_mutation	Average:64.814; most accessible tissue: Zhenshan97 root, score: 81.564	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0322639869	NA	4.85E-16	mr1158	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
vg0322639869	NA	1.32E-10	mr1471	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
vg0322639869	NA	1.55E-10	mr1499	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
vg0322639869	1.50E-06	NA	mr1248_2	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
vg0322639869	5.94E-06	NA	mr1251_2	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
vg0322639869	1.29E-06	NA	mr1263_2	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
vg0322639869	6.13E-06	NA	mr1435_2	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
vg0322639869	1.56E-06	6.25E-07	mr1603_2	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
vg0322639869	NA	2.87E-28	mr1757_2	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
vg0322639869	NA	3.02E-07	mr1762_2	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
vg0322639869	NA	4.54E-10	mr1818_2	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
vg0322639869	NA	6.31E-11	mr1897_2	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
vg0322639869	NA	1.67E-17	mr1927_2	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