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Detailed information for vg1000477617:

Variant ID: vg1000477617 (JBrowse)	Variation Type: SNP
Chromosome: chr10	Position: 477617
Reference Allele: C	Alternative Allele: A
Primary Allele: A	Secondary Allele: C

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

AACCCCTACGTGAGGATCCCTCTCCTCTCTCAAACCGCGTTTTAGTAACCCTGTATTGCTCTGGTAGTTCAAGCTGCACAACACGGCTAGGTGGAGTTAG[C/A]
ACCCTTCTGGTGTCTATCCATTCTCTGTATTGACATCTCCTTGGTGGTTCCTGGGAGAAAAGAATAGATGTGAAGCGAGCAAAGTTAGTAAATGTTGTGA

Reverse complement sequence

TCACAACATTTACTAACTTTGCTCGCTTCACATCTATTCTTTTCTCCCAGGAACCACCAAGGAGATGTCAATACAGAGAATGGATAGACACCAGAAGGGT[G/T]
CTAACTCCACCTAGCCGTGTTGTGCAGCTTGAACTACCAGAGCAATACAGGGTTACTAAAACGCGGTTTGAGAGAGGAGAGGGATCCTCACGTAGGGGTT

Allele Frequencies:

Populations	Population Size	Frequency of A(primary allele)	Frequency of C(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	74.90%	16.80%	0.40%	7.83%	NA
All Indica	2759	94.80%	0.50%	0.62%	4.10%	NA
All Japonica	1512	50.10%	49.40%	0.00%	0.53%	NA
Aus	269	23.00%	3.30%	0.37%	73.23%	NA
Indica I	595	98.50%	0.50%	0.84%	0.17%	NA
Indica II	465	98.10%	0.40%	0.65%	0.86%	NA
Indica III	913	93.20%	0.10%	0.00%	6.68%	NA
Indica Intermediate	786	92.00%	0.90%	1.15%	5.98%	NA
Temperate Japonica	767	21.10%	78.70%	0.00%	0.13%	NA
Tropical Japonica	504	93.30%	6.70%	0.00%	0.00%	NA
Japonica Intermediate	241	51.90%	45.20%	0.00%	2.90%	NA
VI/Aromatic	96	45.80%	9.40%	1.04%	43.75%	NA
Intermediate	90	70.00%	18.90%	0.00%	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
vg1000477617	C -> A	LOC_Os10g01740.1	synonymous_variant ; p.Val18Val; LOW	synonymous_codon	Average:20.211; most accessible tissue: Minghui63 panicle, score: 29.741	N	N	N	N
vg1000477617	C -> DEL	LOC_Os10g01740.1	N	frameshift_variant	Average:20.211; most accessible tissue: Minghui63 panicle, score: 29.741	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1000477617	2.88E-25	9.27E-47	mr1300	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
vg1000477617	8.22E-12	1.36E-16	mr1300	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
vg1000477617	6.98E-27	4.87E-66	mr1310	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
vg1000477617	1.53E-12	9.11E-20	mr1310	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
vg1000477617	1.19E-06	1.44E-06	mr1498	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
vg1000477617	1.40E-34	2.70E-80	mr1926	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
vg1000477617	2.95E-14	1.89E-23	mr1926	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
vg1000477617	4.37E-13	2.49E-19	mr1959	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
vg1000477617	3.24E-09	1.57E-11	mr1959	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
vg1000477617	9.32E-44	4.32E-79	mr1310_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
vg1000477617	1.17E-21	8.88E-34	mr1310_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
vg1000477617	2.38E-20	6.58E-32	mr1959_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
vg1000477617	3.13E-12	1.81E-19	mr1959_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