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Detailed information for vg0405719474:

Variant ID: vg0405719474 (JBrowse)	Variation Type: SNP
Chromosome: chr04	Position: 5719474
Reference Allele: T	Alternative Allele: C
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

CAGGAAACGATGAGATTGGGGATTTTAGAATATTTGCACGGTGACTCCGAGATAACTTAAAACAAACACGAGCTCTCTGATGGTTTTAGGAATTTTTCTC[T/C]
GTGATATCTTGGATTTGGCTTGGAGAGGAAGCTAAAAGAAATTATGTGGAAGGTGGAAACTCAGAGGGAACAAAAGGAATATTGTTGACGAAAAATCCGC

Reverse complement sequence

GCGGATTTTTCGTCAACAATATTCCTTTTGTTCCCTCTGAGTTTCCACCTTCCACATAATTTCTTTTAGCTTCCTCTCCAAGCCAAATCCAAGATATCAC[A/G]
GAGAAAAATTCCTAAAACCATCAGAGAGCTCGTGTTTGTTTTAAGTTATCTCGGAGTCACCGTGCAAATATTCTAAAATCCCCAATCTCATCGTTTCCTG

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	50.10%	8.50%	0.76%	40.61%	NA
All Indica	2759	37.70%	0.40%	1.12%	60.82%	NA
All Japonica	1512	73.30%	24.60%	0.13%	1.92%	NA
Aus	269	41.60%	0.00%	0.74%	57.62%	NA
Indica I	595	9.40%	0.00%	1.68%	88.91%	NA
Indica II	465	57.00%	0.60%	0.65%	41.72%	NA
Indica III	913	46.30%	0.40%	0.99%	52.25%	NA
Indica Intermediate	786	37.70%	0.40%	1.15%	60.81%	NA
Temperate Japonica	767	77.80%	21.90%	0.13%	0.13%	NA
Tropical Japonica	504	59.90%	35.30%	0.20%	4.56%	NA
Japonica Intermediate	241	87.10%	10.80%	0.00%	2.07%	NA
VI/Aromatic	96	53.10%	12.50%	0.00%	34.38%	NA
Intermediate	90	61.10%	11.10%	1.11%	26.67%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0405719474	T -> C	LOC_Os04g10500-LOC_Os04g10530	intergenic_region ; MODIFIER	silent_mutation	Average:50.367; most accessible tissue: Callus, score: 91.094	N	N	N	N
vg0405719474	T -> DEL	N	N	silent_mutation	Average:50.367; most accessible tissue: Callus, score: 91.094	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0405719474	2.98E-06	8.54E-07	mr1035	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
vg0405719474	1.60E-11	NA	mr1062	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
vg0405719474	7.26E-09	4.81E-11	mr1062	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
vg0405719474	3.59E-11	2.69E-10	mr1525	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
vg0405719474	1.26E-08	1.26E-08	mr1525	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
vg0405719474	NA	5.10E-07	mr1626	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
vg0405719474	2.34E-09	NA	mr1035_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
vg0405719474	4.55E-09	3.65E-10	mr1035_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
vg0405719474	1.51E-10	NA	mr1062_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
vg0405719474	2.93E-07	2.32E-09	mr1062_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
vg0405719474	1.31E-11	1.31E-11	mr1525_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
vg0405719474	2.75E-08	2.75E-08	mr1525_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
vg0405719474	5.94E-09	NA	mr1631_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
vg0405719474	3.92E-09	6.41E-11	mr1631_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