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Detailed information for vg1221363597:

Variant ID: vg1221363597 (JBrowse)Variation Type: SNP
Chromosome: chr12Position: 21363597
Reference Allele: AAlternative Allele: C
Primary Allele: ASecondary Allele: C

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


ACATGCATGGACTCCTCAAGAATATGAAACAGGGTAAAGCCGCAGGTTTCACAGAGGATGAACACGGAACTCTATGGAACGGAAAGCGGGTATGCGTTCC[A/C]
GATAGCAGAGAACTTAAACAGCTGATACTTCAGGAAGCTCACGCAAGTCCTTATTCCATTCACCCGGGCAGTACCAAGATGTACTTAGACTTGAAGGAGA

Reverse complement sequence

TCTCCTTCAAGTCTAAGTACATCTTGGTACTGCCCGGGTGAATGGAATAAGGACTTGCGTGAGCTTCCTGAAGTATCAGCTGTTTAAGTTCTCTGCTATC[T/G]
GGAACGCATACCCGCTTTCCGTTCCATAGAGTTCCGTGTTCATCCTCTGTGAAACCTGCGGCTTTACCCTGTTTCATATTCTTGAGGAGTCCATGCATGT

Allele Frequencies:

Populations Population SizeFrequency of A(primary allele) Frequency of C(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 99.10% 0.10% 0.00% 0.72% NA
All Indica  2759 99.90% 0.10% 0.00% 0.00% NA
All Japonica  1512 97.70% 0.10% 0.00% 2.25% NA
Aus  269 98.90% 1.10% 0.00% 0.00% NA
Indica I  595 99.80% 0.20% 0.00% 0.00% NA
Indica II  465 100.00% 0.00% 0.00% 0.00% NA
Indica III  913 99.80% 0.20% 0.00% 0.00% NA
Indica Intermediate  786 100.00% 0.00% 0.00% 0.00% NA
Temperate Japonica  767 96.10% 0.10% 0.00% 3.78% NA
Tropical Japonica  504 99.20% 0.00% 0.00% 0.79% NA
Japonica Intermediate  241 99.60% 0.00% 0.00% 0.41% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 100.00% 0.00% 0.00% 0.00% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg1221363597 A -> C LOC_Os12g35110.1 synonymous_variant ; p.Pro1317Pro; LOW N Average:35.742; most accessible tissue: Minghui63 flag leaf, score: 59.244 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1221363597 3.96E-06 NA mr1817_2 Ind_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