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Why do start coordinates differ by 1 base
19-Nov-2013, 05:21 PM
Post: #1
Why do start coordinates differ by 1 base

S.cerevise YAL012W CDS starts at genomic coordinate:
130799: according to the header of the FASTA format sequence
130798: according to the sgdGene annotated table (

* according to the NCBI the start genomic coordinate of this gene is: 130799 (

Best Regards,

Hello Renana,

Regarding the start genomic coordinate for this gene (and for all genes), out tables use the UCSC Genome Browser table representations where start coordinates are 0-based (eg 130798 for YAL012W), and are converted to 1-based coordinates for display (eg 130799 for YAL012W). I refer you to the section "Database/browser start coordinates differ by 1 base" in the following FAQ from the UCSC Genome Browser

I hope this answers your question regarding the differences in start coordinates for the different information displays.

Thanks again for your interest in GWIPS-viz.

Kind Regards,
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