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Detailed information for vg0209789548:

Variant ID: vg0209789548 (JBrowse)	Variation Type: SNP
Chromosome: chr02	Position: 9789548
Reference Allele: T	Alternative Allele: C
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

TTGTGTTACCAACCGGGACTAAAGATCATCTTTAGTCCCGGTTCGAATGCTGTCAGGACCTGTCAGGCCCCCCCGGGATCTTTAGTCCCGGTTGGTAACA[T/C]
CAACCGGGACTAAAGATCTTAACTTTAGTCCCGGTTGGTATTACCAACCGGGACTAAAGATCCCGGTGATCTTTAGCCCCGGTTGGTGTTACCAACCGGG

Reverse complement sequence

CCCGGTTGGTAACACCAACCGGGGCTAAAGATCACCGGGATCTTTAGTCCCGGTTGGTAATACCAACCGGGACTAAAGTTAAGATCTTTAGTCCCGGTTG[A/G]
TGTTACCAACCGGGACTAAAGATCCCGGGGGGGCCTGACAGGTCCTGACAGCATTCGAACCGGGACTAAAGATGATCTTTAGTCCCGGTTGGTAACACAA

Allele Frequencies:

Populations	Population Size	Frequency of T(primary allele)	Frequency of C(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	64.80%	1.70%	2.03%	31.42%	NA
All Indica	2759	51.90%	0.00%	2.14%	45.99%	NA
All Japonica	1512	91.50%	5.40%	2.18%	0.99%	NA
Aus	269	37.50%	0.00%	0.00%	62.45%	NA
Indica I	595	57.30%	0.00%	1.85%	40.84%	NA
Indica II	465	49.70%	0.00%	1.51%	48.82%	NA
Indica III	913	52.00%	0.00%	1.31%	46.66%	NA
Indica Intermediate	786	48.90%	0.00%	3.69%	47.46%	NA
Temperate Japonica	767	98.70%	0.00%	0.13%	1.17%	NA
Tropical Japonica	504	78.60%	14.70%	5.75%	0.99%	NA
Japonica Intermediate	241	95.40%	2.90%	1.24%	0.41%	NA
VI/Aromatic	96	87.50%	0.00%	0.00%	12.50%	NA
Intermediate	90	71.10%	1.10%	4.44%	23.33%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0209789548	T -> DEL	N	N	silent_mutation	Average:15.817; most accessible tissue: Zhenshan97 root, score: 36.298	N	N	N	N
vg0209789548	T -> C	LOC_Os02g17100.1	upstream_gene_variant ; 756.0bp to feature; MODIFIER	silent_mutation	Average:15.817; most accessible tissue: Zhenshan97 root, score: 36.298	N	N	N	N
vg0209789548	T -> C	LOC_Os02g17090-LOC_Os02g17100	intergenic_region ; MODIFIER	silent_mutation	Average:15.817; most accessible tissue: Zhenshan97 root, score: 36.298	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0209789548	NA	5.45E-06	mr1218	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
vg0209789548	NA	7.35E-06	mr1382	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
vg0209789548	NA	9.38E-07	mr1398	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
vg0209789548	1.67E-06	3.84E-10	mr1422	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
vg0209789548	NA	3.27E-06	mr1583	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
vg0209789548	NA	1.70E-07	mr1696	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