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Detailed information for vg0200562733:

Variant ID: vg0200562733 (JBrowse)Variation Type: SNP
Chromosome: chr02Position: 562733
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


TACTCTTCATAACCCTGCTAGCAGTCTGAACCCGGCCACTGTTGAAAAGCGCTACCATGACAGACATGAACAGGGATGGGCTCGGTACATGCCCTTGTTC[C/T]
ATCATACTGTCAAGTGCCGTCTTTGCATCAGCTGGCTCATTCTTCTTCAGGAAGCTATCAACAAGCAGTGCATGCGATTCAGGGTCAGTACGGACACCAC

Reverse complement sequence

GTGGTGTCCGTACTGACCCTGAATCGCATGCACTGCTTGTTGATAGCTTCCTGAAGAAGAATGAGCCAGCTGATGCAAAGACGGCACTTGACAGTATGAT[G/A]
GAACAAGGGCATGTACCGAGCCCATCCCTGTTCATGTCTGTCATGGTAGCGCTTTTCAACAGTGGCCGGGTTCAGACTGCTAGCAGGGTTATGAAGAGTA

Allele Frequencies:

Populations Population SizeFrequency of C(primary allele) Frequency of T(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 99.70% 0.30% 0.06% 0.00% NA
All Indica  2759 100.00% 0.00% 0.00% 0.00% NA
All Japonica  1512 99.00% 0.90% 0.13% 0.00% NA
Aus  269 100.00% 0.00% 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  913 100.00% 0.00% 0.00% 0.00% NA
Indica Intermediate  786 100.00% 0.00% 0.00% 0.00% NA
Temperate Japonica  767 100.00% 0.00% 0.00% 0.00% NA
Tropical Japonica  504 97.20% 2.60% 0.20% 0.00% NA
Japonica Intermediate  241 99.60% 0.00% 0.41% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 98.90% 0.00% 1.11% 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
vg0200562733 C -> T LOC_Os02g02020.1 missense_variant ; p.Met558Ile; MODERATE nonsynonymous_codon ; M558I Average:73.99; most accessible tissue: Callus, score: 89.161 benign 0.004 TOLERATED 1.00