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Detailed information for vg0709987989:

Variant ID: vg0709987989 (JBrowse)	Variation Type: SNP
Chromosome: chr07	Position: 9987989
Reference Allele: A	Alternative Allele: G
Primary Allele: A	Secondary Allele: G

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

ACCTGGTGACAAAACAGAAATGGGACACGTTTTTCATCATTTTCTGATGAGAATTTTTTTTTTCGCTGACAAAATAATGACAAATTCAAGATCACTCGCA[A/G]
AAAACATAAAAAAAATTGCTGGTTTGTTTCACATCATTATTTGTGAATTTGTGATTGTTAATCAGATCACAAAGCGATTCACGATCAGATCTGTCGTTTC

Reverse complement sequence

GAAACGACAGATCTGATCGTGAATCGCTTTGTGATCTGATTAACAATCACAAATTCACAAATAATGATGTGAAACAAACCAGCAATTTTTTTTATGTTTT[T/C]
TGCGAGTGATCTTGAATTTGTCATTATTTTGTCAGCGAAAAAAAAAATTCTCATCAGAAAATGATGAAAAACGTGTCCCATTTCTGTTTTGTCACCAGGT

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	85.90%	1.00%	1.38%	11.68%	NA
All Indica	2759	88.90%	0.00%	0.07%	11.05%	NA
All Japonica	1512	77.20%	3.20%	3.44%	16.07%	NA
Aus	269	100.00%	0.00%	0.00%	0.00%	NA
Indica I	595	69.10%	0.00%	0.00%	30.92%	NA
Indica II	465	94.40%	0.00%	0.22%	5.38%	NA
Indica III	913	99.70%	0.00%	0.00%	0.33%	NA
Indica Intermediate	786	88.00%	0.00%	0.13%	11.83%	NA
Temperate Japonica	767	65.80%	5.10%	6.26%	22.82%	NA
Tropical Japonica	504	99.00%	0.20%	0.00%	0.79%	NA
Japonica Intermediate	241	68.00%	3.70%	1.66%	26.56%	NA
VI/Aromatic	96	89.60%	0.00%	9.38%	1.04%	NA
Intermediate	90	94.40%	0.00%	2.22%	3.33%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0709987989	A -> DEL	N	N	silent_mutation	Average:56.654; most accessible tissue: Callus, score: 79.611	N	N	N	N
vg0709987989	A -> G	LOC_Os07g16980.1	upstream_gene_variant ; 2084.0bp to feature; MODIFIER	silent_mutation	Average:56.654; most accessible tissue: Callus, score: 79.611	N	N	N	N
vg0709987989	A -> G	LOC_Os07g16970.1	intron_variant ; MODIFIER	silent_mutation	Average:56.654; most accessible tissue: Callus, score: 79.611	N	N	N	N
vg0709987989	A -> G	LOC_Os07g16970.2	intron_variant ; MODIFIER	silent_mutation	Average:56.654; most accessible tissue: Callus, score: 79.611	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0709987989	NA	3.01E-08	mr1624	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
vg0709987989	NA	5.81E-09	mr1624_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
vg0709987989	NA	3.41E-10	mr1733_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
vg0709987989	NA	4.55E-07	mr1736_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
vg0709987989	NA	4.69E-06	mr1736_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
vg0709987989	NA	9.47E-06	mr1739_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
vg0709987989	NA	3.85E-08	mr1741_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
vg0709987989	NA	4.00E-06	mr1751_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
vg0709987989	NA	1.28E-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
vg0709987989	NA	1.20E-06	mr1887_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