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Detailed information for vg1006789704:

Variant ID: vg1006789704 (JBrowse)	Variation Type: SNP
Chromosome: chr10	Position: 6789704
Reference Allele: T	Alternative Allele: C
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

ATTTTGTGATGAACAACACCATTAATTTTAAAAACATAAGGTGCACTTCCATTGTTTATCGTTCTATCGATAGTTGCACCCATAGAGGTGAAAGCAAACA[T/C]
AGAGTTGTAAGATCGCACCTGCCTAAGAAATCTCTTTGAACGTGCATCTCCATTAAATTTCAACAATGTTTTAAGAGGTTCTGGAGGTTCACGTAGTTTT

Reverse complement sequence

AAAACTACGTGAACCTCCAGAACCTCTTAAAACATTGTTGAAATTTAATGGAGATGCACGTTCAAAGAGATTTCTTAGGCAGGTGCGATCTTACAACTCT[A/G]
TGTTTGCTTTCACCTCTATGGGTGCAACTATCGATAGAACGATAAACAATGGAAGTGCACCTTATGTTTTTAAAATTAATGGTGTTGTTCATCACAAAAT

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	85.80%	5.80%	0.30%	8.10%	NA
All Indica	2759	99.50%	0.50%	0.00%	0.00%	NA
All Japonica	1512	63.60%	10.60%	0.66%	25.13%	NA
Aus	269	99.60%	0.40%	0.00%	0.00%	NA
Indica I	595	100.00%	0.00%	0.00%	0.00%	NA
Indica II	465	100.00%	0.00%	0.00%	0.00%	NA
Indica III	913	99.10%	0.90%	0.00%	0.00%	NA
Indica Intermediate	786	99.10%	0.90%	0.00%	0.00%	NA
Temperate Japonica	767	91.10%	0.30%	0.13%	8.47%	NA
Tropical Japonica	504	21.20%	28.20%	1.59%	49.01%	NA
Japonica Intermediate	241	64.30%	7.10%	0.41%	28.22%	NA
VI/Aromatic	96	14.60%	85.40%	0.00%	0.00%	NA
Intermediate	90	76.70%	15.60%	4.44%	3.33%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1006789704	T -> C	LOC_Os10g12174.1	missense_variant ; p.Met313Val; MODERATE	nonsynonymous_codon ; M313V	Average:7.143; most accessible tissue: Callus, score: 29.028	benign	0.662	DELETERIOUS	0.01
vg1006789704	T -> DEL	LOC_Os10g12174.1	N	frameshift_variant	Average:7.143; most accessible tissue: Callus, score: 29.028	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1006789704	NA	4.69E-06	mr1057	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
vg1006789704	NA	7.98E-06	mr1124	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
vg1006789704	4.65E-07	NA	mr1136	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
vg1006789704	NA	3.56E-08	mr1136	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
vg1006789704	9.57E-06	9.57E-06	mr1173	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
vg1006789704	NA	7.36E-11	mr1570	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
vg1006789704	NA	8.31E-06	mr1596	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
vg1006789704	NA	2.11E-07	mr1047_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
vg1006789704	NA	4.96E-10	mr1057_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
vg1006789704	NA	7.92E-07	mr1188_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
vg1006789704	4.25E-06	4.25E-06	mr1333_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
vg1006789704	NA	7.57E-06	mr1850_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