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Detailed information for vg0123776530:

Variant ID: vg0123776530 (JBrowse)	Variation Type: SNP
Chromosome: chr01	Position: 23776530
Reference Allele: A	Alternative Allele: C
Primary Allele: A	Secondary Allele: C

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

CAAACATATACTGCACTAGTTCTCAACGAGGGTTGCATTGCATTGCGTAGCGTGGACTATCACTAACACACAATGGCTAGAATGGCTAGAACTCCAGTTC[A/C]
TCCACGATCGTCCTCGATTGTAGCTGCATTCACTTACCTTTTGCTAGTCCTCTTCCGAGACGCCATCACCACCGCAGCTGCATCTCCCAAAGCTCCGGCA

Reverse complement sequence

TGCCGGAGCTTTGGGAGATGCAGCTGCGGTGGTGATGGCGTCTCGGAAGAGGACTAGCAAAAGGTAAGTGAATGCAGCTACAATCGAGGACGATCGTGGA[T/G]
GAACTGGAGTTCTAGCCATTCTAGCCATTGTGTGTTAGTGATAGTCCACGCTACGCAATGCAATGCAACCCTCGTTGAGAACTAGTGCAGTATATGTTTG

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	43.60%	0.00%	0.15%	56.22%	NA
All Indica	2759	9.90%	0.00%	0.18%	89.89%	NA
All Japonica	1512	92.10%	0.00%	0.00%	7.94%	NA
Aus	269	92.20%	0.00%	0.00%	7.81%	NA
Indica I	595	2.90%	0.00%	0.34%	96.81%	NA
Indica II	465	6.00%	0.00%	0.00%	93.98%	NA
Indica III	913	11.30%	0.00%	0.11%	88.61%	NA
Indica Intermediate	786	16.00%	0.00%	0.25%	83.72%	NA
Temperate Japonica	767	99.50%	0.00%	0.00%	0.52%	NA
Tropical Japonica	504	79.00%	0.00%	0.00%	21.03%	NA
Japonica Intermediate	241	95.90%	0.00%	0.00%	4.15%	NA
VI/Aromatic	96	99.00%	0.00%	0.00%	1.04%	NA
Intermediate	90	56.70%	2.20%	2.22%	38.89%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0123776530	A -> DEL	LOC_Os01g41930.1	N	frameshift_variant	Average:66.115; most accessible tissue: Minghui63 root, score: 85.669	N	N	N	N
vg0123776530	A -> C	LOC_Os01g41930.1	missense_variant ; p.His10Pro; MODERATE	nonsynonymous_codon ; H10P	Average:66.115; most accessible tissue: Minghui63 root, score: 85.669	unknown	unknown	TOLERATED	0.29

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0123776530	NA	6.20E-07	mr1850	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
vg0123776530	NA	6.51E-07	mr1870_2	Ind_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