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Detailed information for vg0710326904:

Variant ID: vg0710326904 (JBrowse)	Variation Type: SNP
Chromosome: chr07	Position: 10326904
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

GCCCAATACACCAGATCAATCCTTTTCTTCAACAACATCCAAAGGTACATATATTAAGATAAATCTTCAACATGATCAATATAGCTCTTCAGCTCAGTGA[C/T]
AACATCCATCAGTACTCTTAAATTCGAAACGAGCACCTCCACAAAGTACTCTTGCCTAGCTCGAACCTTCAAAAGGTACAATAATTCCACCCATCAGTCT

Reverse complement sequence

AGACTGATGGGTGGAATTATTGTACCTTTTGAAGGTTCGAGCTAGGCAAGAGTACTTTGTGGAGGTGCTCGTTTCGAATTTAAGAGTACTGATGGATGTT[G/A]
TCACTGAGCTGAAGAGCTATATTGATCATGTTGAAGATTTATCTTAATATATGTACCTTTGGATGTTGTTGAAGAAAAGGATTGATCTGGTGTATTGGGC

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	36.20%	3.90%	0.49%	59.37%	NA
All Indica	2759	6.70%	0.00%	0.80%	92.50%	NA
All Japonica	1512	82.30%	12.10%	0.00%	5.56%	NA
Aus	269	60.20%	0.00%	0.37%	39.41%	NA
Indica I	595	4.00%	0.00%	0.67%	95.29%	NA
Indica II	465	5.20%	0.00%	1.08%	93.76%	NA
Indica III	913	3.30%	0.10%	0.77%	95.84%	NA
Indica Intermediate	786	13.50%	0.00%	0.76%	85.75%	NA
Temperate Japonica	767	79.00%	19.30%	0.00%	1.69%	NA
Tropical Japonica	504	86.70%	0.20%	0.00%	13.10%	NA
Japonica Intermediate	241	83.80%	14.10%	0.00%	2.07%	NA
VI/Aromatic	96	79.20%	1.00%	0.00%	19.79%	NA
Intermediate	90	50.00%	0.00%	0.00%	50.00%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0710326904	C -> DEL	LOC_Os07g17490.1	N	frameshift_variant	Average:8.961; most accessible tissue: Callus, score: 43.869	N	N	N	N
vg0710326904	C -> T	LOC_Os07g17490.1	missense_variant ; p.Val370Ile; MODERATE	nonsynonymous_codon ; V370I	Average:8.961; most accessible tissue: Callus, score: 43.869	unknown	unknown	TOLERATED	0.39

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0710326904	NA	5.02E-18	Awn_length	All	Not	Breeding signatures of rice improvement revealed by a genomic variation map from a large germplasm collection, Proc Natl Acad Sci USA, 112(39): E5411-E5419, PMID:26358652
vg0710326904	NA	1.54E-09	Awn_length	Jap_All	Not	Breeding signatures of rice improvement revealed by a genomic variation map from a large germplasm collection, Proc Natl Acad Sci USA, 112(39): E5411-E5419, PMID:26358652
vg0710326904	NA	6.37E-06	mr1006	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
vg0710326904	NA	5.64E-06	mr1052	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
vg0710326904	8.28E-06	NA	mr1549	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
vg0710326904	NA	1.09E-09	mr1549	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
vg0710326904	NA	9.75E-14	mr1624	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
vg0710326904	NA	8.28E-10	mr1624	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
vg0710326904	NA	1.11E-07	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
vg0710326904	NA	3.69E-11	mr1624_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
vg0710326904	NA	2.43E-07	mr1624_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
vg0710326904	NA	8.03E-06	mr1736_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
vg0710326904	NA	1.13E-08	mr1741_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