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Detailed information for vg1000865327:

Variant ID: vg1000865327 (JBrowse)	Variation Type: SNP
Chromosome: chr10	Position: 865327
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

TTTGGCAATAAAAGGTGGACCAGAGTGCAATTAACTCTTGTTTTTTTCCTACATTTAATACTTCATATATATGTCCAAACATTCGATGTGACAGCGTGAA[C/T]
AATTTTGTTTTGTGACTAAGGGTGTGTTCGGACCCAAGGGTTCCCAACACCTCTCCATCGTTTTCCGCGTGCACGCTTTTCAAACTGCTAAACGGTGTGT

Reverse complement sequence

ACACACCGTTTAGCAGTTTGAAAAGCGTGCACGCGGAAAACGATGGAGAGGTGTTGGGAACCCTTGGGTCCGAACACACCCTTAGTCACAAAACAAAATT[G/A]
TTCACGCTGTCACATCGAATGTTTGGACATATATATGAAGTATTAAATGTAGGAAAAAAACAAGAGTTAATTGCACTCTGGTCCACCTTTTATTGCCAAA

Allele Frequencies:

Populations	Population Size	Frequency of C(primary allele)	Frequency of T(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	95.10%	1.10%	0.99%	2.77%	NA
All Indica	2759	98.70%	0.00%	0.25%	1.05%	NA
All Japonica	1512	94.60%	3.60%	1.59%	0.26%	NA
Aus	269	58.70%	0.00%	5.58%	35.69%	NA
Indica I	595	98.70%	0.00%	0.34%	1.01%	NA
Indica II	465	98.70%	0.00%	0.00%	1.29%	NA
Indica III	913	99.20%	0.00%	0.22%	0.55%	NA
Indica Intermediate	786	98.10%	0.00%	0.38%	1.53%	NA
Temperate Japonica	767	90.70%	6.40%	2.48%	0.39%	NA
Tropical Japonica	504	99.80%	0.00%	0.20%	0.00%	NA
Japonica Intermediate	241	95.90%	2.10%	1.66%	0.41%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	96.70%	0.00%	1.11%	2.22%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1000865327	C -> T	LOC_Os10g02380.1	upstream_gene_variant ; 1062.0bp to feature; MODIFIER	silent_mutation	Average:42.218; most accessible tissue: Zhenshan97 panicle, score: 72.468	N	N	N	N
vg1000865327	C -> T	LOC_Os10g02360-LOC_Os10g02380	intergenic_region ; MODIFIER	silent_mutation	Average:42.218; most accessible tissue: Zhenshan97 panicle, score: 72.468	N	N	N	N
vg1000865327	C -> DEL	N	N	silent_mutation	Average:42.218; most accessible tissue: Zhenshan97 panicle, score: 72.468	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1000865327	NA	4.19E-06	mr1354	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
vg1000865327	NA	5.81E-09	mr1549	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
vg1000865327	3.87E-07	1.75E-08	mr1550	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
vg1000865327	NA	1.10E-11	mr1757	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
vg1000865327	NA	3.81E-06	mr1045_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
vg1000865327	NA	6.92E-09	mr1549_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
vg1000865327	NA	1.33E-06	mr1550_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
vg1000865327	NA	2.52E-08	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