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Detailed information for vg1006613497:

Variant ID: vg1006613497 (JBrowse)	Variation Type: SNP
Chromosome: chr10	Position: 6613497
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

AGGAAGTCCTTCATCCCGACTGGCTGGCCAACTCAATCCTGGTTCAGAAGAAAACGGGACAATGGCGCATGTGTGTTGACTACACTAACTTCAGCAAGTC[C/T]
TGTCCCAAAGATCCTTTTGGGTTGCCTCGCATTGACCAGGTAGTTGACTCAATAGCCGGCTGCGAGCTTCTCAGCTTTTTGGATTGCTACTCAGGTTACC

Reverse complement sequence

GGTAACCTGAGTAGCAATCCAAAAAGCTGAGAAGCTCGCAGCCGGCTATTGAGTCAACTACCTGGTCAATGCGAGGCAACCCAAAAGGATCTTTGGGACA[G/A]
GACTTGCTGAAGTTAGTGTAGTCAACACACATGCGCCATTGTCCCGTTTTCTTCTGAACCAGGATTGAGTTGGCCAGCCAGTCGGGATGAAGGACTTCCT

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	36.30%	5.40%	9.29%	48.98%	NA
All Indica	2759	39.20%	0.00%	6.78%	54.01%	NA
All Japonica	1512	38.50%	16.50%	7.41%	37.63%	NA
Aus	269	4.10%	0.00%	42.75%	53.16%	NA
Indica I	595	11.90%	0.00%	5.04%	83.03%	NA
Indica II	465	61.30%	0.20%	4.30%	34.19%	NA
Indica III	913	41.40%	0.00%	9.31%	49.29%	NA
Indica Intermediate	786	44.10%	0.00%	6.62%	49.24%	NA
Temperate Japonica	767	49.00%	31.60%	8.60%	10.82%	NA
Tropical Japonica	504	15.30%	0.20%	6.75%	77.78%	NA
Japonica Intermediate	241	53.50%	2.50%	4.98%	39.00%	NA
VI/Aromatic	96	9.40%	0.00%	13.54%	77.08%	NA
Intermediate	90	37.80%	5.60%	13.33%	43.33%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1006613497	C -> T	LOC_Os10g11920.1	synonymous_variant ; p.Ser307Ser; LOW	synonymous_codon	Average:9.405; most accessible tissue: Callus, score: 25.425	N	N	N	N
vg1006613497	C -> DEL	LOC_Os10g11920.1	N	frameshift_variant	Average:9.405; most accessible tissue: Callus, score: 25.425	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1006613497	4.99E-06	NA	mr1768	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
vg1006613497	3.44E-13	1.73E-31	mr1768_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
vg1006613497	3.70E-07	2.08E-11	mr1768_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