Schema for Subgenomic RNA Modif. - Subgenomic RNA Modifications from Kim et al. 2020: gRNA S 3a E M 6 7a 7b 8 N
  Database: wuhCor1    Primary Table: kimRnaMod Data last updated: 2020-04-10
Big Bed File: /gbdb/wuhCor1/bbi/kim2020/
Item Count: 41
Format description: BED6+5 with additional fields for category count and median values, and sample matrix fields
chromNC_045512v2Reference sequence chromosome or scaffold
chromStart25355Start position in chromosome
chromEnd25358End position in chromosome
name25357Position of modified nucleotide
score999Score from 0-1000, typically derived from total of median value from all categories
strand++ or - for strand. Use . if not applicable
name2GCUCAAASequence context of modified nucleotide
expCount10Number of categories
expScores0.312,0.146,0.571,0.0,0.0,0.0,0.0,0.0,0.0,0.0Comma separated list of category values
_dataOffset291Offset of sample data in data matrix file, for boxplot on details page
_dataLen51Length of sample data row in data matrix file

Sample Rows

Subgenomic RNA Modif. (kimRnaMod) Track Description


This track shows the locations of RNA-modifications as determined by Nanopore sequencing Kim et al, Cell 2020.

Display Conventions and Configuration

Very small tickmarks indicate the position of the RNA modifications on the genome. One has to zoom in to basepair level detail to see their exact extent. A small barchart over the tick indicates the fraction of transcripts that are modified relative to the un-modified transcripts. E.g. frac=0.3 means that 30% of the transcripts were modified. There is one barchart per transcript.

Data Access

The raw data can be explored interactively with the Table Browser, or combined with other datasets in the Data Integrator tool. For automated analysis, the genome annotation is stored in a bigBed file that can be downloaded from the download server.

Annotations can be converted from binary to ASCII text by our command-line tool bigBedToBed. Instructions for downloading this command can be found on our utilities page. The tool can also be used to obtain features within a given range without downloading the file, for example:

bigBedToBed -chrom=NC_045512v2 -start=0 -end=29902 stdout

Please refer to our mailing list archives for questions, or our Data Access FAQ for more information.


Thanks to Hyeshik Chang for preparing and sharing custom tracks.


The architecture of SARS-CoV-2 transcriptome. Cell 2020. pre-proof